Download Molecular 3D Viewer (Molecular Structure)
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?
School - 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
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
are stored in the pdbfiles directory
Load and view 3-D structures
CHEMIX 3-D Molecular viewer allow you to load *.pdb structures, rotate
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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