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Basicity of Aliphatic Amines

Basicity of Aliphatic Amines

Amines can behave as Brønsted–Lowry bases by accepting a proton from the acid to form corresponding conjugate acids. Due to a lone pair of nonbonding electrons, aliphatic amines can also act as Lewis bases by forming a covalent bond with an electrophile.
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates...

Amino acids

Amino acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible...

Basicity of Heterocyclic Aromatic Amines

Basicity of Heterocyclic Aromatic Amines

Heterocyclic amines, where the N atom is a part of an alicyclic system, are similar in basicity to alkylamines. Interestingly, the heterocyclic amine having a nitrogen atom as part of an aromatic ring has much less basicity than its corresponding alicyclic counterpart. For this reason, as presented in Figure 1, piperidine (pKb = 2.8) is significantly more basic than pyridine (pKb = 8.8).

NMR Spectroscopy Of Amines

NMR Spectroscopy Of Amines

In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is...

Aldehydes and Ketones with Amines: Imine Formation Mechanism

Aldehydes and Ketones with Amines: Imine Formation Mechanism

Imine formation involves the addition of carbonyl compounds to a primary amine. It begins with the generation of carbinolamine through a series of steps involving an initial nucleophilic attack and then several proton transfer reactions. The second part includes the elimination of water, as a leaving group, to give the imine.
Imines are formed under mildly acidic conditions. A pH of 4.5 is ideal for the reaction.
If the pH is low or the solution is too acidic, the reaction slows down in the...

Basicity of Aromatic Amines

Basicity of Aromatic Amines

The basicity of aromatic amines is much weaker than that of aliphatic amines due to the involvement of the lone pair of electrons over the N atom in resonance with the aryl rings. Generally, the electron-donating ability of any substituents on the aryl ring of aromatic amines increases the basicity of the amine by increasing electron density, and hence the availability of lone pair on the nitrogen. On the other hand, electron-withdrawing functional groups on the aryl ring of amines decrease the...

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Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

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Amino acid deprotonation rates from classical force fields.

Themis Lazaridis¹, Aliasghar Sepehri¹

¹Department of Chemistry, City College of New York/CUNY, 160 Convent Ave., New York, New York 10031, USA.

The Journal of Chemical Physics

|September 1, 2022

Summary

This study introduces a novel computational method to estimate proton deprotonation rates for amino acid side chains. The approach utilizes molecular simulations and Marcus theory to calculate reaction barriers, crucial for understanding proton transport mechanisms.

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Determination of the Gas-phase Acidities of Oligopeptides

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Determination of the Gas-phase Acidities of Oligopeptides

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

Area of Science:

Biophysical Chemistry
Computational Biochemistry
Molecular Dynamics

Background:

Acid ionization constants (pK_a) are well-studied for amino acid side chains.
Protonation/deprotonation rates (k_on/k_off) are critical for biological processes like proton transport.
Classical force fields cannot directly simulate bond making/breaking in proton transfer.

Purpose of the Study:

To develop a computational method for estimating proton deprotonation rates.
To apply the method to key amino acids (Glu, Asp, His) in various environments.
To investigate the role of deprotonation rates in membrane protein function.

Main Methods:

Utilized an extension of Marcus theory for electron transfer.
Integrated molecular simulations to capture environmental effects.
Estimated deprotonation rates by calculating free energy barriers from energy gap statistics.

Main Results:

Developed a method to estimate deprotonation rates using pK_a fitting and simulation data.
Applied the method to Glu, Asp, and His in solution.
Successfully applied the method to M2 proton channel, bacteriorhodopsin, and cytochrome c oxidase.

Conclusions:

The presented method provides a viable approach to estimate proton deprotonation rates.
This method can aid in understanding the mechanisms of proton channels and coupled transport proteins.
Environmental effects on deprotonation rates can be effectively modeled.