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Related Concept Videos

Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

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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...
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Gibbs Free Energy02:39

Gibbs Free Energy

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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...
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Energy Diagrams - I01:14

Energy Diagrams - I

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The dynamics of a mechanical system can be easily understood by interpreting a potential energy diagram. Since energy is a scalar quantity, the interpretation of the dynamics of the system becomes even simpler.
Take the example of a skater on a parabolic ramp. The potential energy at different points along the ramp will be proportional to the height of the ramp, which varies quadratically with the horizontal position on the ramp. As the skater moves down the ramp from the highest position,...
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Gibbs Free Energy and Thermodynamic Favorability02:23

Gibbs Free Energy and Thermodynamic Favorability

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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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Arrhenius Plots02:34

Arrhenius Plots

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The Arrhenius equation relates the activation energy and the rate constant, k, for chemical reactions. In the Arrhenius equation, k = Ae−Ea/RT, R is the ideal gas constant, which has a value of 8.314 J/mol·K, T is the temperature on the kelvin scale, Ea is the activation energy in J/mole, e is the constant 2.7183, and A is a constant called the frequency factor, which is related to the frequency of collisions and the orientation of the reacting molecules.
The Arrhenius equation can...
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Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

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The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
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Related Experiment Video

Updated: Apr 26, 2026

A Femtoliter Droplet Array for Massively Parallel Protein Synthesis from Single DNA Molecules
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Accelerated weight histogram method for exploring free energy landscapes.

V Lindahl1, J Lidmar1, B Hess1

  • 1Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm, Sweden.

The Journal of Chemical Physics
|August 3, 2014
PubMed
Summary

Calculating free energies in molecular simulations is challenging. The new accelerated weight histogram (AWH) method efficiently explores complex systems, improving free energy landscape analysis for applications like protein folding.

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Calculating free energies is crucial but difficult in molecular simulations.
  • Complex systems require enhanced sampling methods to explore free energy landscapes.
  • Existing methods face challenges in efficiency and applicability.

Purpose of the Study:

  • Introduce and demonstrate the accelerated weight histogram (AWH) method for efficient free energy calculations.
  • Showcase AWH's general applicability and potential for further extensions.
  • Provide practical guidelines for setting up and running AWH simulations.

Main Methods:

  • Utilized the accelerated weight histogram (AWH) method, an enhanced sampling technique.
  • Employed adaptive biasing with a probability weight histogram for efficient free energy updates.
  • Applied a non-uniform, free energy dependent target distribution in reaction coordinate space.

Main Results:

  • Demonstrated AWH efficiency in calculating potential of mean force in one and multiple dimensions.
  • Successfully applied AWH to molecular dynamics simulations of lithium acetate in solution.
  • Showcased AWH's utility in studying the folding of chignolin, a 10-residue peptide.

Conclusions:

  • The AWH method offers an efficient and general approach for free energy calculations in molecular simulations.
  • AWH facilitates exploration of complex free energy landscapes, aiding in the study of systems like protein folding.
  • The method's formulation supports further development and analysis within the field of enhanced sampling.