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Related Concept Videos

Basicity of Aliphatic Amines01:21

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 higher...
Amino acids03:42

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 for...
Acidity and Basicity of Carboxylic Acid Derivatives01:25

Acidity and Basicity of Carboxylic Acid Derivatives

Carboxylic acids are the strongest among organic acids, as they readily lose the hydroxyl proton to form a resonance-stabilized carboxylate ion. In comparison, the acid derivatives lack acidic hydrogens directly attached to a functional group. In these compounds, the acidic nature arises from their ability to lose α hydrogens, making them weakly acidic.
The relative acidic strength of the derivatives can be explained based on the extent of resonance stabilization of the conjugate base. The...
Basicity of Aromatic Amines01:18

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...
Basicity of Heterocyclic Aromatic Amines01:25

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).
Molecular Structure and Acidity02:34

Molecular Structure and Acidity

An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...

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Determination of the Gas-phase Acidities of Oligopeptides
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Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between

Joanna Makowska1, Katarzyna Bagińska, Adam Liwo

  • 1Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.

Biopolymers
|July 12, 2008
PubMed
Summary

The study investigated how ionizable groups and solvents affect acid-base properties in alanine-based peptides. Molecular dynamics simulations accurately predicted experimental results, outperforming Monte Carlo methods.

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Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Area of Science:

  • Biophysical Chemistry
  • Computational Chemistry
  • Peptide Science

Background:

  • Understanding peptide acid-base properties is crucial for biological function and drug design.
  • Solvent effects and ionizable end groups significantly influence peptide behavior.
  • Accurate theoretical modeling is needed to predict these properties.

Purpose of the Study:

  • To evaluate the impact of ionizable end groups and solvents on acid-base properties of alanine-based peptides.
  • To assess the performance of two computational methods (EDMC/PB/pH and MD/GB/pH) in simulating peptide pH-metric titrations.
  • To analyze the influence of charged side chains on peptide pKa values.

Main Methods:

  • Potentiometry was used to determine the acid-base properties of three alanine-based peptides (KAK, OAD, KAE) in water and methanol.
  • Electrostatically driven Monte Carlo (EDMC/PB/pH) and molecular dynamics (MD/GB/pH) methods were employed for theoretical simulations.
  • Nuclear Magnetic Resonance (NMR) data was incorporated to refine conformational searches in the MD/GB/pH approach.

Main Results:

  • Peptide pKa values were significantly lower than those of isolated amino acids, attributed to electrostatic fields from charged lysine or ornithine side chains.
  • The MD/GB/pH method successfully reproduced experimental titration curves, with improved accuracy when NMR restraints were included.
  • The EDMC/PB/pH method showed poorer agreement with experimental data.

Conclusions:

  • The electrostatic environment within peptides plays a critical role in modulating acid-base properties.
  • Molecular dynamics simulations, particularly with NMR restraints, offer a reliable approach for predicting peptide titration behavior.
  • Computational methods are valuable tools for studying peptide chemistry, aiding in the design of peptide-based therapeutics.