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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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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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Thermodynamic Potentials

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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...
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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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Thermodynamic Systems01:06

Thermodynamic Systems

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A thermodynamic system is a set of objects whose thermodynamic properties are of interest. The system is considered to be embedded in its surroundings or the environment. The system and its environment can exchange heat and do work on each other through a boundary that separates them. However, the immediate surroundings of the system interact with it directly and therefore have a much stronger influence on its behavior and properties.
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Maxwell's thermodynamic relations are very useful in solving problems in thermodynamics. Each of Maxwell's relations relates a partial differential between quantities that can be hard to measure experimentally to a partial differential between quantities that can be easily measured. These relations are a set of equations derivable from the symmetry of the second derivatives and the thermodynamic potentials.
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SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations.

Tai-Sung Lee1, Omid Jahanmahin1, Saikat Pal1

  • 1Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine (IQB), and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.

The Journal of Physical Chemistry. B
|December 9, 2025
PubMed
Summary
This summary is machine-generated.

Sampling adaptive thermodynamic integration (SAMTI) enhances free energy calculations by integrating serial tempering, variance adaptive resampling, replica exchange, and alchemical enhanced sampling. This method significantly reduces statistical error and improves computational efficiency for molecular design.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Physical Chemistry

Background:

  • Conventional thermodynamic integration (TI) methods for calculating alchemical free energies face challenges like poor phase-space overlap and inefficient resource allocation.
  • These limitations lead to slow convergence and high statistical uncertainty in free energy calculations.

Purpose of the Study:

  • To introduce Sampling Adaptive Thermodynamic Integration (SAMTI), a unified computational framework designed to overcome the limitations of conventional TI methods.
  • To enhance the accuracy and efficiency of alchemical free energy calculations.

Main Methods:

  • SAMTI integrates serial tempering (ST) with a fine-grained alchemical grid for phase-space continuity.
  • Variance adaptive resampling (VAR) dynamically allocates computational effort to high-uncertainty regions.
  • Replica exchange (RE) enhances conformational sampling, and alchemical enhanced sampling (ACES) resolves kinetic bottlenecks.

Main Results:

  • SAMTI variants reduced statistical error by 40-75% compared to conventional TI across eight molecular systems.
  • The complete ST+VAR+RE (mACES) configuration achieved chemical accuracy (σΔG < 0.1 kcal/mol) within 10 ns for complex systems.
  • SAMTI demonstrated superior computational efficiency through adaptive resource allocation and faster convergence.

Conclusions:

  • SAMTI provides a robust, automated, and reliable solution for alchemical and conformational sampling challenges in free energy calculations.
  • SAMTI establishes a new benchmark for free energy calculations, accelerating molecular design in drug discovery and materials science.