Download Molecular 3D Viewer (Molecular Structure) Software

Chemistry Software Download


Is it possible to deduce physical properties of a molecule only by knowing its structure? Fairly good predictions can be done by combining the knowledge of electronegativity and the understanding of molecular symmetry. Predictions of a molecule ability to dissolve in other molecules can be estimated this way. Related to this, the expression "Like dissolves like" means that, in general, nonpolar substances dissolve in nonpolar solvents and polar substances dissolve in polar solvents. But what's polarity?

CHEMIX School - Molecular 3D viewer

Molecular 3D viewer


The polarity of a molecule is a result of how atoms are arranged in the molecule and their electronegativity. In a non ionic compound, a "real" molecule, the atoms are connected by covalent bonds in which are more or less polar.

1)If all the bonds in a molecule are nonpolar, the molecule is nonpolar. (e.g. CH4)
2)If all the bonds in a symmetrically arranged molecule has equal polarity, the overall polarity of the molecule will cancel out. (e.g. CCl4)
3) If the bonds in a molecule are not symmetrically arranged, then the arrangement of the bonds determines the polarity of the molecule. In the water molecule the bonds are not symmetrically arranged (104.5deg). As a result, the oxygen end of the molecule is slightly more negative than the hydrogen end, and the molecule is polar.

Fig. Water molecule polarity

Water molecule polarity

The Protein Data-Bank format - PDB

The PDB format is a 3-D file format that intentionally was designed for dealing with protein structures. CHEMIX basically use this format for smaller structures limited to less than 2500 atoms. A lot of free PDB download sources are available on the Internet. You can easily build your own 3-D library by downloading from these sources. In CHEMIX these files are stored in the pdbfiles directory

Load and view 3-D structures

CHEMIX 3-D Molecular viewer allow you to load *.pdb structures, rotate and size both the molecule and its atoms. It is also possible to peek into the text content of these files (File info).

Size By these push buttons you may change the size of both molecule and atoms.

Statistics displays statistical data

File info displays some of the text content in these files e.g. COMPND and REMARK.

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