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Related Concept Videos

Chemical Equilibria: Systematic Approach to Equilibrium Calculations01:21

Chemical Equilibria: Systematic Approach to Equilibrium Calculations

1.0K
Equilibrium calculations for systems involving multiple equilibria are often complex. For example, to calculate the solubility of a sparingly soluble salt in an aqueous solution in the presence of a common ion, one must consider all the equilibria in this solution. Calculations for these systems can be complicated and tedious, so a systematic approach with a series of steps is often helpful. The process is detailed below.
The first step is to identify all the chemical reactions involved, The...
1.0K
Chemical Equilibria: Redefining Equilibrium Constant01:20

Chemical Equilibria: Redefining Equilibrium Constant

848
The effect of an inert salt on the solubility of a sparingly soluble salt is known as the salt effect. The degree of the salt effect varies with the ionic strength of the solution, which in turn depends on the activity of the species in the solution. The activity is expressed as the product of concentration and the activity coefficient of the species.
To calculate the equilibrium constants of solutions of moderately high ionic strength, one must account for the salt effect. This redefined...
848
Calculating the Equilibrium Constant02:46

Calculating the Equilibrium Constant

34.0K
The equilibrium constant for a reaction is calculated from the equilibrium concentrations (or pressures) of its reactants and products. If these concentrations are known, the calculation simply involves their substitution into the Kc expression.
For example, gaseous nitrogen dioxide forms dinitrogen tetroxide according to this equation:
34.0K
Thermodynamic Potentials01:26

Thermodynamic Potentials

1.0K
Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...
1.0K
The Equilibrium Constant03:10

The Equilibrium Constant

50.8K
Consider the oxidation of sulfur dioxide:
50.8K
Calculating Equilibrium Concentrations02:05

Calculating Equilibrium Concentrations

49.6K
Being able to calculate equilibrium concentrations is essential to many areas of science and technology—for example, in the formulation and dosing of pharmaceutical products. After a drug is ingested or injected, it is typically involved in several chemical equilibria that affect its ultimate concentration in the body system of interest. Knowledge of the quantitative aspects of these equilibria is required to compute a dosage amount that will solicit the desired therapeutic effect.
A more...
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Collecting Variable-concentration Isothermal Titration Calorimetry Datasets in Order to Determine Binding Mechanisms
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eQuilibrator 3.0: a database solution for thermodynamic constant estimation.

Moritz E Beber1,2, Mattia G Gollub3, Dana Mozaffari3,4

  • 1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark.

Nucleic Acids Research
|December 1, 2021
PubMed
Summary
This summary is machine-generated.

The eQuilibrator database now features a Python interface with a larger compound library and improved performance. This update enhances thermodynamic modeling accessibility and integration for systems biology research.

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Area of Science:

  • Biochemistry
  • Systems Biology
  • Computational Biology

Background:

  • eQuilibrator is a web-based database for biochemical equilibrium constants and Gibbs free energies.
  • The original design had limitations in handling large compound databases and lacked a scalable Application Programming Interface (API).

Purpose of the Study:

  • To report updates to the eQuilibrator database, including a new Python interface.
  • To enhance the database's capacity, performance, and integration capabilities for the systems biology community.

Main Methods:

  • Developed a new Python-based interface for the eQuilibrator database.
  • Expanded the compound database by 100-fold and enabled the addition of novel compounds.
  • Implemented improvements in speed, memory usage, and added correction for Mg2+ ion concentrations.

Main Results:

  • The new Python interface offers a significantly larger compound database and improved computational efficiency.
  • The interface can now compute the covariance matrix of uncertainty between estimates.
  • Demonstrated advantages and applications of the new features in metabolic modeling.

Conclusions:

  • The updated eQuilibrator database and Python interface make thermodynamic modeling more accessible.
  • Facilitates seamless integration of eQuilibrator into other software platforms for systems biology applications.