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Gibbs Free Energy and Thermodynamic Favorability

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:

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Transition State Theory

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Transition-state theory, also known as activated-complex theory, provides a molecular-level explanation of reaction rates in both gas-phase and solution-phase reactions. It extends earlier kinetic models by considering the formation of a short-lived, high-energy configuration during a reaction.The progress of a chemical reaction can be represented using a reaction profile, which plots potential energy against the reaction coordinate. As two reactant molecules approach one another, their...

Energy Diagrams, Transition States, and Intermediates

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Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products. Peaks on the energy diagram represent stable structures with measurable lifetimes, while other...

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The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔGrxn is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
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Related Experiment Video

Updated: Jul 2, 2026

Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level

Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level

Published on: September 26, 2016

Diffusive reaction dynamics on invariant free energy profiles.

Sergei V Krivov¹, Martin Karplus

¹Laboratoiré de Chimie Biophysique, Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, 67000 Strasbourg, France. krivov@isis-ulp.org

Proceedings of the National Academy of Sciences of the United States of America

|September 6, 2008

Summary

This study introduces a novel method combining free energy profiles to determine diffusion coefficients in complex reactions like protein folding. This approach enhances the analysis of reaction coordinates and protein dynamics.

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Area of Science:

Computational Chemistry
Biophysics
Molecular Dynamics

Background:

Determining activation free energy is crucial for understanding protein folding and entropy-driven reactions.
Existing methods using molecular dynamics simulations face challenges with reaction coordinate transformations.

Purpose of the Study:

To develop a robust method for calculating coordinate-dependent diffusion coefficients.
To introduce an invariant method for analyzing free energy profiles in complex systems.

Main Methods:

Combining minimum-cut-based free energy profiles (F(C)) with histogram-based profiles (F(H)).
Utilizing equilibrium molecular dynamics simulations.
Introducing a "natural coordinate" for invariant analysis.

Main Results:

The proposed method extracts free energies and diffusive preexponential factors along reaction coordinates.
F(C) profiles are invariant to reaction coordinate transformations, enabling invariant partitioning of configuration space.
Demonstrated on a model 1D system, alanine dipeptide, and a double beta-hairpin miniprotein.

Conclusions:

The approach provides a reliable way to determine diffusion coefficients in complex molecular systems.
It offers a criterion to assess the suitability of a chosen reaction coordinate for studying protein folding and dynamics.