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Related Concept Videos

Gibbs Free Energy02:39

Gibbs Free Energy

One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
An Introduction to Free Energy01:05

An Introduction to Free Energy

How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these energy transfers. Scientists call this free energy Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. According to the second law of thermodynamics, all energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy. Gibbs free energy...
Gibbs Free Energy and Thermodynamic Favorability02:23

Gibbs Free Energy and Thermodynamic Favorability

The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
Estimation of the Physical Quantities01:05

Estimation of the Physical Quantities

On many occasions, physicists, other scientists, and engineers need to make estimates of a particular quantity. These are sometimes referred to as guesstimates, order-of-magnitude approximations, back-of-the-envelope calculations, or Fermi calculations. The physicist Enrico Fermi was famous for his ability to estimate various kinds of data with surprising precision. Estimating does not mean guessing a number or a formula at random. Instead, estimation means using prior experience and sound...
The Reaction Gibbs Energy01:29

The Reaction Gibbs Energy

The reaction Gibbs energy (ΔrG) is a crucial parameter that determines whether a reaction will occur spontaneously or not. It can be used to categorize reactions into two types: exergonic and endergonic.Exergonic reactions are those in which ΔrG is less than zero. This implies that these reactions can occur spontaneously without an external input of energy. In biological systems, a typical example of an exergonic reaction is the oxidation of carbohydrates. This reaction produces simple...

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Determining the Contribution of the Energy Systems During Exercise
11:15

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Published on: March 20, 2012

Consistent estimation of Gibbs energy using component contributions.

Elad Noor1, Hulda S Haraldsdóttir, Ron Milo

  • 1Plant Sciences Department, Weizmann Institute of Science, Rehovot, Israel.

Plos Computational Biology
|July 23, 2013
PubMed
Summary

This study introduces a hybrid method to accurately estimate standard Gibbs energies for metabolic reactions. By combining group and reactant contributions, it improves thermodynamic modeling for a better understanding of metabolism.

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Area of Science:

  • Biochemistry
  • Systems Biology
  • Chemical Thermodynamics

Background:

  • Standard Gibbs energy of reaction is crucial for metabolic modeling, enabling thermodynamic constraints on reaction rates and metabolite concentrations.
  • Existing genome-scale solutions often rely on group contribution methods, which offer broad coverage but reduced precision.
  • There is a need for accurate and consistent estimation of standard Gibbs energies across diverse metabolic models.

Purpose of the Study:

  • To develop a novel method for estimating standard Gibbs energies of metabolic reactions by combining group and reactant contributions.
  • To improve the accuracy and consistency of thermodynamic predictions in metabolic modeling.
  • To provide a framework that enhances the application of thermodynamic data in understanding metabolism.

Main Methods:

  • A hybrid approach was developed, decomposing reactions into two parts to apply both group contribution and reactant contribution methods.
  • Priority is given to more accurate reactant contributions, ensuring thermodynamic consistency and adherence to the first law of thermodynamics.
  • The method was validated using cross-validation to assess the accuracy of the estimated standard Gibbs energies.

Main Results:

  • The combined method significantly enhances the accuracy of standard Gibbs energy estimations compared to traditional group contribution methods.
  • A notable 80% reduction in median absolute residual was observed for reactions estimated solely by reactant contributions.
  • The framework provides reliable estimates of standard reaction Gibbs energy and associated confidence intervals.

Conclusions:

  • The developed hybrid method offers a more precise and thermodynamically consistent way to estimate standard Gibbs energies for metabolic reactions.
  • This approach facilitates the integration of accurate thermodynamic data into genome-scale metabolic models.
  • The availability of the framework and source code is expected to promote wider use of thermodynamic insights in metabolic research.