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Free energy—abbreviated as G for the scientist Gibbs who discovered it—is a measurement of useful energy that can be extracted from a reaction to do work. It is the energy in a chemical reaction that is available after entropy is accounted for. Reactions that take in energy are considered endergonic and reactions that release energy are exergonic. Plants carry out endergonic reactions by taking in sunlight and carbon dioxide to produce glucose and oxygen. Animals, in turn, break...
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The free energy change associated with dissolving a solute in a liter of solvent is called the free energy of a solution, ΔGsolution. The overall ΔGsolution is expressed as the balance of ΔGinteraction against the always-favorable free-energy of mixing, ΔGmixing. Solution formation is favorable if  ΔGsolution is less than zero, whereas it is unfavorable if ΔGsolution is greater than zero. In short, for a solution to form and complete dissolution to take place,...
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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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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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Nonequilibrium Binding Free Energy Simulations: Minimizing Dissipation.

Eleonora Serra1,2, Alessia Ghidini3, Sergio Decherchi4

  • 1Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy.

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This summary is machine-generated.

Estimating protein-ligand binding free energy using nonequilibrium simulations is challenging due to irreversible work. Optimizing water models and path collective variables significantly improves free energy estimator convergence.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Dynamics

Background:

  • Equilibrium free energy estimation methods are established.
  • Nonequilibrium simulations offer parallelization but face convergence challenges.
  • Protein-ligand binding free energy estimation is crucial in drug discovery.

Purpose of the Study:

  • Investigate challenges in protein-ligand binding free energy estimation via nonequilibrium simulations.
  • Analyze the impact of simulation parameters on estimator convergence.
  • Provide strategies to enhance simulation efficiency.

Main Methods:

  • Nonequilibrium molecular dynamics simulations.
  • Physical path sampling for protein-ligand binding.
  • Analysis of free energy estimators (e.g., Crooks equation).
  • Systematic variation of water models and path collective variables.

Main Results:

  • Irreversible work generated during simulations hinders estimator convergence.
  • Water models critically affect the convergence rate of free energy estimators.
  • Parametrization of path collective variables significantly impacts convergence.
  • Identified key factors influencing dissipation in simulations.

Conclusions:

  • Nonequilibrium simulations require careful parameter selection for reliable free energy calculations.
  • Optimized water models and collective variables enhance convergence speed.
  • Practical strategies can minimize dissipation and improve computational efficiency.