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Atomic Structure

Atomic Structure

The Greek philosopher Democritus proposed that everything on Earth is made up of tiny particles called atomos, Greek for "indivisible," from which the modern term "atom" is derived. In the 19th century, John Dalton proposed the atomic theory that is still largely correct today. He put forth five postulates to explain how atoms made up the world around us. (1) All matter is composed of infinitely small particles or atoms. (2) All atoms of a given element are identical to one...

Atomic Structure

Atomic Structure

Electronic Structure of Atoms

Electronic Structure of Atoms

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...

Structure of Amines

Structure of Amines

The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are...

Atomic Orbitals

Atomic Orbitals

An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.

The Aufbau Principle and Hund's Rule

The Aufbau Principle and Hund's Rule

To determine the electron configuration for any particular atom, we can build the structures in the order of atomic numbers. Beginning with hydrogen, and continuing across the periods of the periodic table, we add one proton at a time to the nucleus and one electron to the proper subshell until we have described the electron configurations of all the elements. This procedure is called the aufbau principle, from the German word aufbau (“to build up”). Each added electron occupies the...

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Related Experiment Video

Updated: Dec 28, 2025

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

atomium-a Python structure parser.

Sam M Ireland¹, Andrew C R Martin¹

¹Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.

Bioinformatics (Oxford, England)

|February 12, 2020

Summary

This summary is machine-generated.

Atomium is a new Python library for handling structural biology file formats like PDB, mmCIF, and MMTF. It offers improved features and API design for parsing, manipulating, and saving macromolecular structure data.

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Last Updated: Dec 28, 2025

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

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Published on: April 13, 2022

Atom Probe Tomography Analysis of Exsolved Mineral Phases

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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Area of Science:

Structural biology
Computational biology
Bioinformatics

Background:

Macromolecular structure data is crucial in structural biology.
Traditional Protein Data Bank (PDB) format has limitations.
Emerging formats like PDBML, mmCIF, and MMTF offer enhanced capabilities.

Purpose of the Study:

Introduce atomium, a novel Python library for structural biology file formats.
Provide a web service, pdb2json, for consistent data representation.
Facilitate easier parsing, manipulation, and saving of macromolecular structure data.

Main Methods:

Developed atomium as a lightweight Python library.
Implemented support for PDB, mmCIF, and MMTF file formats.
Integrated atomium into the pdb2json web service for Protein Data Bank data conversion.

Main Results:

Atomium provides efficient parsing, manipulation, and saving of multiple structural file formats.
The pdb2json service offers a unified JSON representation for the entire Protein Data Bank.
Atomium demonstrates performance equivalent to BioPython with enhanced features and API design.

Conclusions:

Atomium offers a modern and versatile solution for handling structural biology data.
The library and associated web service streamline access and utilization of macromolecular structure information.
Atomium represents a significant advancement in bioinformatics tools for structural data management.