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Related Concept Videos

Electronic Structure of Atoms02:28

Electronic Structure of Atoms

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An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...
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Lewis symbols can be used to indicate the formation of covalent bonds, which are shown in Lewis structures—drawings that describe the bonding in molecules and polyatomic ions. The periodic table can be used to predict the number of valence electrons in an atom and the number of bonds that will be formed to reach an octet. Group 18 elements, such as argon and helium, have filled electron configurations and thus rarely participate in chemical bonding. However, atoms from group 17, such as...
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In some cases, there are seemingly more than one valid Lewis structures for molecules and polyatomic ions. The concept of formal charges can be used to help predict the most appropriate Lewis structure when more than one reasonable structure exists.
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Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing...
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Updated: May 12, 2025

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
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PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures.

Ondřej Schindler1,2, Tomáš Svoboda1,2,3, Adrián Rošinec1,2,3

  • 1CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.

Nucleic Acids Research
|May 10, 2025
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Summary
This summary is machine-generated.

Calculating partial atomic charges for protein structures is crucial for understanding chemical reactivity. The new PDBCharges web application offers a fast and accessible method for computing these charges from Protein Data Bank (PDB) structures.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biochemistry

Background:

  • The Protein Data Bank (PDB) houses over 230,000 experimentally determined protein structures.
  • Partial atomic charges are essential for understanding protein chemical reactivity, derived from electron density distributions.
  • Existing methods for calculating partial atomic charges for large and variable protein structures are limited in accuracy and universality.

Purpose of the Study:

  • To introduce PDBCharges, a novel web application for rapid calculation of partial atomic charges for protein structures.
  • To provide a user-friendly tool for accessing and visualizing atomic charge data from the PDB.

Main Methods:

  • Utilized the GFN1-xTB semi-empirical quantum-mechanical method for charge calculations.
  • Ensured GFN1-xTB results reproduce established PBE0/TZVP/CM5 charges.
  • Developed a web application for easy access and integration with the Mol* Viewer.

Main Results:

  • PDBCharges enables quick calculation of partial atomic charges for PDB protein structures.
  • The application provides downloadable charge data in standard formats.
  • Integrated visualization capabilities using the Mol* Viewer for interactive exploration.

Conclusions:

  • PDBCharges addresses the need for an accurate and accessible tool for protein partial atomic charge calculation.
  • The web application facilitates research in protein chemistry and structural biology.
  • Freely available and without login requirements, PDBCharges promotes widespread adoption and use.