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Calculations of Electric Potential II01:27

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An electric dipole is a system of two equal but opposite charges, separated by a fixed distance. This system is used to model many real-world systems, including atomic and molecular interactions. One of these systems is the water molecule, but only under certain circumstances. These circumstances are met inside a microwave oven, where electric fields with alternating directions make the water molecules change orientation. This vibration is equivalent to heat at the molecular level.
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Atomic Charge Calculator III: a modern platform for calculating partial atomic charges.

Tomáš Raček1,2, Martin Pilát3, Ondřej Schindler1,2

  • 1National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.

Nucleic Acids Research
|April 27, 2026
PubMed
Summary

Atomic Charge Calculator III (ACC III) is a new web tool for calculating partial atomic charges in molecules. It offers 20 methods, interactive visualization, and supports FAIR data standards for broader use in chemistry and biology.

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Area of Science:

  • Computational chemistry
  • Chemoinformatics
  • Bioinformatics

Background:

  • Partial atomic charges are crucial for understanding molecular electrostatic properties and interactions.
  • Fast and accurate empirical methods for calculating these charges are essential for various scientific disciplines.
  • Previous versions of the Atomic Charge Calculator have been valuable resources.

Purpose of the Study:

  • To introduce Atomic Charge Calculator III (ACC III), an advanced web application for computing partial atomic charges.
  • To provide a comprehensive tool supporting diverse molecular systems and a wide range of empirical charge calculation methods.
  • To enhance the accessibility and usability of partial atomic charge calculations for researchers.

Main Methods:

  • Implementation of 20 established and state-of-the-art empirical charge calculation methods, including SQE+qp with updated parameters.
  • Integration of the Mol* viewer for interactive 3D visualization of molecular structures and charge distributions.
  • Development of a web interface, a programmatic API, and a command-line version for flexible deployment.

Main Results:

  • ACC III successfully computes partial atomic charges for small organic molecules and proteins.
  • The platform enables embedding computed charges into mmCIF files, adhering to FAIR data principles.
  • The tool offers seamless integration into automated workflows and supports community-standard data distribution.

Conclusions:

  • ACC III represents a significant advancement in computational tools for molecular electrostatic analysis.
  • The application's accessibility, comprehensive features, and FAIR data support will benefit computational chemistry, chemoinformatics, and bioinformatics.
  • The freely available, no-login service promotes widespread adoption and collaboration in molecular sciences.