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Related Concept Videos

Potential Due to a Polarized Object01:29

Potential Due to a Polarized Object

A neutral atom consists of a positively charged nucleus surrounded by a negatively charged electron cloud. When placed in an external electric field, the external electric force pulls the electrons and nucleus apart, opposite to the intrinsic attraction between the nucleus and the electrons. The opposing forces balance each other with a slight shift between the center of masses of the nucleus and the electron cloud, resulting in a polarized atom. On the other hand, a few molecules, like water,...
Poisson's And Laplace's Equation01:25

Poisson's And Laplace's Equation

The electric potential of the system can be calculated by relating it to the electric charge densities that give rise to the electric potential. The differential form of Gauss's law expresses the electric field's divergence in terms of the electric charge density.
Electric Field of a Continuous Line Charge01:19

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In physics, symmetry in a system means that something in the considered system remains unchanged due to a specific operation to which it is subjected. For example, consider a horizontal square. The square looks the same if its right and left sides are interchanged. Hence, it is symmetric under a right-left interchange.
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Electric Field of a Non Uniformly Charged Sphere01:22

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Continuous Charge Distributions01:17

Continuous Charge Distributions

Imagine a bucket of water. It contains many molecules, of the order of 1026 molecules. Thus, although it contains discrete elements (molecules) at the microscopic level, macroscopically, it can be considered continuous. Small volume elements of water, infinitesimal compared to the bulk of the bucket's volume, still contain many molecules. Under this framework, quantized matter is approximated as continuous for practical purposes.
The electric charge can also be subjected to an analogical...
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Electrostatic Boundary Conditions

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Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

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Published on: September 1, 2023

Continuum polarizable force field within the Poisson-Boltzmann framework.

Yu-Hong Tan1, Chunhu Tan, Junmei Wang

  • 1Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.

The Journal of Physical Chemistry. B
|May 30, 2008
PubMed
Summary
This summary is machine-generated.

Researchers developed new nonbonded parameters for a continuum polarizable force field, showing accuracy comparable to high-level quantum mechanics methods. Optimized atomic cavity radii improve solvation free energy predictions for organic molecules.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Physical Chemistry

Background:

  • Accurate molecular modeling requires precise force fields.
  • Continuum polarizable force fields offer a balance between accuracy and computational cost.
  • Developing robust nonbonded parameters is crucial for force field performance.

Purpose of the Study:

  • To develop and validate a new set of nonbonded parameters for a continuum polarizable force field.
  • To assess the model's accuracy against quantum mechanics calculations and experimental data.
  • To optimize and test atomic cavity radii for improved solvation energy predictions.

Main Methods:

  • Development of nonbonded parameters for a continuum polarizable force field.
  • Comparison of the model's electronic response and dipole moments with B3LYP/cc-pVTZ.
  • Testing of Amber van der Waals parameter interchangeability between explicit and continuum models.
  • Optimization of atomic cavity radii using experimental solvation free energies for 177 molecules.
  • Validation of optimized radii against 176 independent test molecules using Poisson-Boltzmann calculations.

Main Results:

  • The new continuum polarizable model demonstrates consistency with B3LYP/cc-pVTZ for electronic response and dipole moments.
  • The model shows good agreement with MP2/cc-pVTZ for dimer binding energies (<0.9 kcal/mol deviation in aqueous dielectric).
  • Optimized Poisson-Boltzmann atomic cavity radii exhibit excellent transferability, yielding an overall RMSD of 1.30 kcal/mol and an average unsigned error of 1.07 kcal/mol across 353 molecules.

Conclusions:

  • The developed nonbonded parameters and optimized cavity radii provide a reliable continuum polarizable force field.
  • The model's accuracy is comparable to high-level quantum mechanical methods for various molecular properties.
  • This framework is suitable for constructing comprehensive protein and nucleic acid force fields.