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Related Concept Videos

Molecular Structure and Acidity02:34

Molecular Structure and Acidity

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An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...
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Acid Strength and Molecular Structure03:05

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Binary Acids and Bases
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
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Lewis Structures of Molecular Compounds and Polyatomic Ions02:54

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To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:
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Structure of Benzene: Molecular Orbital Model01:18

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According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
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VSEPR Theory for Determination of Electron Pair Geometries
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Molecular Models02:00

Molecular Models

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Related Experiment Video

Updated: Jan 30, 2026

Processing of Bulk Nanocrystalline Metals at the US Army Research Laboratory
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pdb-tools: a swiss army knife for molecular structures.

João P G L M Rodrigues1, João M C Teixeira2, Mikaël Trellet3

  • 1Structural Biology, Stanford University School of Medicine, Stanford, California, 94305, USA.

F1000Research
|February 2, 2019
PubMed
Summary
This summary is machine-generated.

The pdb-tools offer Python scripts for easy command-line manipulation of molecular structure data in Protein Data Bank (PDB) format. This open-source collection enables efficient editing, conversion, and validation of PDB files without external dependencies.

Keywords:
PDBPythonbioinformaticschemistrymacromoleculesprotein structurestructural biology

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics

Background:

  • The Protein Data Bank (PDB) is a crucial repository for molecular structure data.
  • Efficient manipulation of PDB files is essential for structural bioinformatics research.
  • Existing tools may have limitations in terms of ease of use, dependencies, or specific functionalities.

Purpose of the Study:

  • To introduce a versatile suite of command-line Python scripts for processing PDB files.
  • To provide researchers with a simple yet efficient toolset for PDB data management.
  • To offer an open-source solution for common PDB file manipulation tasks.

Main Methods:

  • Development of a collection of Python scripts.
  • Implementation using Python with no external dependencies.
  • Command-line interface for user interaction.

Main Results:

  • The pdb-tools facilitate editing, conversion, and validation of PDB files.
  • Scripts operate efficiently from the command-line.
  • The tools are implemented in pure Python, ensuring broad compatibility.

Conclusions:

  • The pdb-tools provide a valuable, dependency-free resource for researchers working with PDB data.
  • The suite simplifies common tasks in molecular structure data handling.
  • Freely available under the Apache License, promoting accessibility and adoption.