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Related Experiment Video

Updated: Oct 31, 2025

Combining Solid-state and Solution-based Techniques: Synthesis and Reactivity of ChalcogenidoplumbatesII or IV

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Published on: December 29, 2016

Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges.

Andreia Fortuna^1,2, Paulo J Costa¹

¹BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal.

Journal of Chemical Information and Modeling

|June 29, 2021

Summary

This study optimizes Poisson-Boltzmann Surface Area (PBSA) calculations for halogenated compounds by developing compatible extra point (EP) models and atomic radii. This improves the accuracy of molecular mechanics/molecular dynamics simulations for halogen bonds.

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Area of Science:

Computational Chemistry
Molecular Modeling
Biophysics

Background:

Off-center point charges (extra points, EPs) are used in molecular mechanics/molecular dynamics (MM/MD) to model the electrostatic potential of halogens.
Poisson-Boltzmann Surface Area (PBSA) calculations estimate solvation free energies but rely on empirical atomic radii.
Existing EP models and compatible radii for halogens in PBSA are limited, hindering accurate simulations of halogenated compounds.

Purpose of the Study:

To assess and optimize PBSA calculations for estimating solvation free energies (ΔGsolv) of halogenated compounds in water.
To develop and validate compatible Poisson-Boltzmann (PB) radii for chlorine, bromine, and iodine within various extra point (EP) models.
To enhance the applicability of EP models within the general AMBER force field (GAFF) and introduce optimized halogen PB radii for the CHARMM general force field (CGenFF).

Main Methods:

Evaluated the performance of PBSA calculations for solvation free energy estimation using different EP models for halogens.
Optimized halogen PB radii (Cl, Br, I) for each EP model to improve accuracy.
Applied and validated EP models within the GAFF and CGenFF frameworks.

Main Results:

Demonstrated the impact of different EP models and optimized PB radii on the accuracy of solvation free energy calculations.
Provided the first set of optimized halogen PB radii for CGenFF, compatible with EP models.
Showcased improved performance of PBSA for halogenated compounds when using optimized parameters.

Conclusions:

Optimized halogen PB radii and EP models significantly improve the accuracy of PBSA calculations for halogenated compounds.
The developed parameters enhance the utility of MM/MD simulations for studying halogen bonds and related phenomena.
This work contributes to more reliable computational predictions for molecules containing halogens.