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Related Concept Videos

Thermodynamic Potentials01:26

Thermodynamic Potentials

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...
Thermodynamics: Chemical Potential and Activity01:10

Thermodynamics: Chemical Potential and Activity

The effective concentration of a species in a solution can be expressed precisely in terms of its activity. Activity considers the effect of electrolytes present in the vicinity of the species of interest and depends on the ionic strength of the solution. The activity of a species is expressed as the product of molar concentration and the activity coefficient of the species.
The thermodynamic equilibrium constant is more accurately defined in terms of activity rather than concentration.
Maxwell's Thermodynamic Relations01:23

Maxwell's Thermodynamic Relations

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.
All thermodynamic potentials are exact differentials. Therefore, their second-order...
The Entropy as a State Function01:14

The Entropy as a State Function

Consider an arbitrary process that moves between two specific states (A and B) in a cyclic manner. This process is reversible and broken down into smaller parts that each follow a Carnot cycle. A Carnot cycle has two isothermal (constant temperature) processes. During these processes, the ratio of the amount of heat transferred to their respective temperature remains constant. The other two processes in the Carnot cycle are also reversible but adiabatic, which means they occur without any heat...
Thermodynamic Processes01:25

Thermodynamic Processes

A thermodynamic process is a path through a sequence of states that takes a system from an initial state to a final state. In a cyclic process, the system returns to its initial state, so the changes in state properties and state functions (ΔT, Δp, ΔV, ΔU, ΔH) over one complete cycle are zero. However, heat and work transfers can still occur during the cycle, and the net heat and net work over the cycle need not be zero.A reversible process occurs when the system is infinitesimally close to...
Path Between Thermodynamics States01:21

Path Between Thermodynamics States

Consider the two thermodynamic processes involving an ideal gas that are represented by paths AC and ABC in Figure 1:

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations.

Thomas Steinbrecher1, InSuk Joung, David A Case

  • 1Institut für Physikalische Chemie, Universität Karlsruhe, Karlsruhe, Germany. thomas.steinbrecher@kit.edu

Journal of Computational Chemistry
|September 29, 2011
PubMed
Summary
This summary is machine-generated.

Soft-core potentials in molecular dynamics simulations improve free energy calculations by preventing singularities. One-step transformations offer a simpler and accurate method for estimating solvation free energies.

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics Simulations
  • Thermodynamics

Background:

  • Molecular dynamics simulations enable the calculation of thermodynamic quantities for small molecules.
  • Thermodynamic integration (TI) can face instabilities due to particle creation/annihilation, known as the 'singularity' problem.

Purpose of the Study:

  • To investigate the use of soft-core potential functions to mitigate singularity issues in TI calculations.
  • To compare the efficiency and accuracy of one-step versus two-step transformations for free energy calculations.
  • To determine recommended parameter values for soft-core Lennard-Jones and Coulomb potentials.

Main Methods:

  • Employed soft-core potential functions to maintain finite pairwise interaction energies during simulations.
  • Performed molecular dynamics-based free energy calculations, specifically focusing on solvation free energies.
  • Compared one-step (simultaneous modification of electrostatic and van der Waals forces) and two-step transformations.

Main Results:

  • Soft-core potentials effectively address singularity problems, leading to smoother free energy curves.
  • Recommended values for soft-core parameters α(LJ) and β(C) were established.
  • One-step transformations demonstrated suitability and convenience for numerical integration in many cases.

Conclusions:

  • Soft-core potentials are crucial for stable and accurate free energy calculations in molecular dynamics.
  • The one-step transformation approach provides a practical and reliable method for estimating solvation free energies.
  • This study offers guidance on parameter selection and transformation strategies for enhanced computational efficiency.