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Related Concept Videos

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...
Alkyl Halides02:45

Alkyl Halides

Structural Properties
Alkyl halides are halogen-substituted alkanes wherein one or more hydrogen atoms of an alkane is replaced by a halogen atom such as fluorine, chlorine, bromine, or iodine. The carbon atom in an alkyl halide is bonded to the halogen atom, which is sp3-hybridized and exhibits a tetrahedral shape.
Unlike alkyl halides, compounds in which a halogen atom is bonded to an sp2 -hybridized carbon atom of a carbon-carbon double bond (C=C) are called vinyl halides. Whereas aryl...
Acid Halides to Amides: Aminolysis01:07

Acid Halides to Amides: Aminolysis

Aminolysis is a nucleophilic acyl substitution reaction, where ammonia or amines act as nucleophiles to give the substitution product. Acid halides react with ammonia, primary amines, and secondary amines to yield primary, secondary, and tertiary amides, respectively.
In the first step of the aminolysis mechanism, the amine attacks the carbonyl carbon of the acyl chloride to form a tetrahedral intermediate. In the second step, the carbonyl group is re-formed with the elimination of a chloride...
Acid Halides to Carboxylic Acids: Hydrolysis01:01

Acid Halides to Carboxylic Acids: Hydrolysis

Hydrolysis of acid halides is a nucleophilic acyl substitution reaction in which acid halides react with water to give carboxylic acids. The reaction occurs readily and does not require acid or a base catalyst.
As shown below, the mechanism involves a nucleophilic attack by water at the carbonyl carbon to form a tetrahedral intermediate. This is followed by the reformation of the carbon–oxygen π bond along with the departure of a halide ion. A final proton transfer step yields carboxylic acid...
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...
Water: A Bronsted-Lowry Acid and Base02:30

Water: A Bronsted-Lowry Acid and Base

The reaction between a Brønsted-Lowry acid and water is called acid ionization. For example, when hydrogen fluoride dissolves in water and ionizes, protons are transferred from hydrogen fluoride molecules to water molecules, yielding hydronium ions and fluoride ions:

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Related Experiment Video

Updated: Jun 27, 2026

Solubility of Hydrophobic Compounds in Aqueous Solution Using Combinations of Self-assembling Peptide and Amino Acid
05:08

Solubility of Hydrophobic Compounds in Aqueous Solution Using Combinations of Self-assembling Peptide and Amino Acid

Published on: September 20, 2017

Ion-specific interactions between halides and basic amino acids in water.

Jan Heyda1, Tomás Hrobárik, Pavel Jungwirth

  • 1Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Complex Molecular Systems and Biomolecules, Flemingovo nam. 2, 16610 Prague 6, Czech Republic.

The Journal of Physical Chemistry. A
|December 5, 2008
PubMed
Summary
This summary is machine-generated.

Small anions like fluoride show strong affinity for positively charged amino acid groups, unlike heavier halides. This specific ion effect, observed in molecular dynamics simulations, also applies to protein surfaces.

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Determination of the Gas-phase Acidities of Oligopeptides
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Determination of the Gas-phase Acidities of Oligopeptides

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Last Updated: Jun 27, 2026

Solubility of Hydrophobic Compounds in Aqueous Solution Using Combinations of Self-assembling Peptide and Amino Acid
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Determination of the Gas-phase Acidities of Oligopeptides
11:00

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

Area of Science:

  • Biophysical Chemistry
  • Computational Chemistry
  • Surface Science

Background:

  • Specific ion effects are crucial for understanding ion-biomolecule interactions.
  • Amino acid surfaces present unique environments for ion adsorption.
  • Previous studies have not fully elucidated halide behavior at amino acid interfaces.

Purpose of the Study:

  • To investigate the ion-specific behavior of halides at the surfaces of aqueous basic amino acids.
  • To quantify the interactions between different halide ions and amino acid functional groups.
  • To predict the implications of these interactions for hydrated protein surfaces.

Main Methods:

  • Molecular dynamics (MD) simulations were performed.
  • Both nonpolarizable and polarizable force fields were employed for accuracy.
  • Analysis included density plots, cumulative sums, and ion residence times.

Main Results:

  • Small anions (e.g., fluoride) exhibit a strong affinity for positively charged amino acid groups (guanidinium > imidazolium > ammonium).
  • Larger, softer anions (e.g., iodide) show weak attraction to nonpolar amino acid regions.
  • Ion-group interactions are local and not excessively strong.

Conclusions:

  • Halide ion behavior at amino acid surfaces is ion-specific and depends on ion size and polarizability.
  • The observed effects are additive and transferable to hydrated protein surfaces.
  • This work provides a quantitative understanding of specific ion effects at biomolecular interfaces.