PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing

  • 0Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou 310052, China.

Summary

This summary is machine-generated.

Related Concept Videos

Molecular Models 02:00

37.8K

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.

Skeletal Model

Simpler two-dimensional representations of chemical compounds are accomplished using skeletal models. The illustration shows only the molecular framework or bonds without explicitly showing the atoms. In this representation, many of the carbon atoms...

Molecular Shapes 01:18

56.7K

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...

VSEPR Theory 02:37

9.0K

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...

Newman Projections 02:06

16.4K

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...

Predicting Molecular Geometry 02:27

34.0K

VSEPR Theory for Determination of Electron Pair Geometries

The following procedure uses VSEPR theory to determine the electron pair geometries and the molecular structures:


Write the Lewis structure of the molecule or polyatomic ion.
Count the number of electron groups (lone pairs and bonds) around the central atom. A single, double, or triple bond counts as one region of electron density.
Identify the electron-pair geometry based on the number of electron groups: linear, trigonal planar,...

VSEPR Theory and the Basic Shapes 02:52

67.4K

Overview of VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure, including approximate bond angles around a central atom, of a molecule from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them....