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Extraction: Effects of pH

Extraction: Effects of pH

Consider a neutral form of an amine, B, with a partition coefficient, K, in a liquid mixture containing organic and aqueous phases. The pH of the aqueous phase affects the charge on acidic and basic solutes, and the charged form is usually more soluble in the aqueous phase. Suppose the conjugate acid form of the amine is soluble only in the aqueous phase while the base form is soluble in both phases. Then the distribution coefficient, D, can be given as the ratio of amine concentration in the...

Extraction: Partition and Distribution Coefficients

Extraction: Partition and Distribution Coefficients

The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
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Model Approaches for Pharmacokinetic Data: Compartment Models

Model Approaches for Pharmacokinetic Data: Compartment Models

Compartmental analysis is a widely adopted approach to characterizing drug pharmacokinetics. It uses compartment models that conceptualize the body as a collection of reversibly communicating compartments, each representing a group of tissues exhibiting similar drug distribution characteristics. The movement rate of the drug between these compartments is typically described by first-order kinetics.
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Physiological Pharmacokinetic Models: Assumption with Protein Binding

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Physiological models with protein binding in pharmacokinetics offer a sophisticated approach to understanding drug disposition. These models consider drug-protein interactions, enabling them to effectively predict drug concentrations in different organs and tissues. This precision aids in accurate drug dosing, providing a significant advantage over conventional models. A key process within these models is equilibration, which ensures that drug concentrations achieve a steady state within the...

Mass Spectrometry of Amines

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In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic aliphatic amines show...

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

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This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
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Related Experiment Video

Updated: Jul 13, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Amino acid partitioning using a Fiedler vector model.

S J Shepherd¹, C B Beggs, S Jones

¹Medical Biophysics Group, School of Engineering, Design and Technology, University of Bradford, BD71DP Bradford, UK. S.J.Shepherd@Bradford.ac.uk

European Biophysics Journal : EBJ

|July 5, 2007

Summary

This study introduces a novel Fiedler vector model to categorize amino acids based on hydrophobicity and polarity. The model successfully partitions amino acid groups, confirming previous findings and validating eigenvector use.

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Published on: April 13, 2022

Area of Science:

Biophysics
Computational Biology
Biochemistry

Background:

Amino acid categorization is crucial for understanding protein structure and function.
Existing models for amino acid classification have limitations.
The Miyazawa-Jernigan matrix provides a basis for biophysical property analysis.

Purpose of the Study:

To develop a new Fiedler vector model for amino acid categorization.
To partition amino acid residues into distinct hydrophobic and polar groups.
To validate the use of eigenvectors in amino acid group partitioning.

Main Methods:

Utilized the Miyazawa-Jernigan matrix as the foundation for the model.
Employed Fiedler vector analysis for categorization.
Grouped amino acids into hydrophobic (LFI, MVWCY) and polar (HATGP, RQSNEDK) sets.

Main Results:

Successfully categorized amino acids into four distinct groups based on hydrophobicity and polarity.
The Fiedler vector model independently confirmed findings by Wang and Wang.
Demonstrated the validity of using eigenvectors for partitioning amino acid groups.
The model's partitioning of amino acids into (LFI), (MVWCY), (HATGP), and (RQSNEDK) groups was effective.

Conclusions:

The Fiedler vector model offers a robust method for amino acid categorization.
Eigenvector-based partitioning is a valid approach for classifying amino acids.
This model supports and expands upon previous research in amino acid classification.