Can someone explain the following types of molecules and predict their structure and shape?
It will help my understanding if you could provide an example.
AX3E,AX5 and AX6
note that A = central atom and X = bonding atoms.
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It will depend on the number of lone electron pairs as well.
For example: $BCl_3$ will be triangular planar as it has no lone electron pairs.
$NH_3$ however will be triangular based-pyramidal because there are 3 bonded pairs of electrons and one lone electron pair.
Basically, it comes down to the number of electron pairs (both bonded and unbonded) around the central atom.
Two electron pairs - Linear
Three electron pairs - Triangular planar
Four electron pairs - Tetrahedral
Five electron pairs - Triangular based bi-pyramidal (it's like triangular planar, but with one on top and one below, or two triangular pyramids with their base stuck together)
Six electron pairs - Octahedral (Square based bi-pyramidal)
Those geometries include the lone electron pairs. For the molecular geometry, you will then need to exclude the electron pair.
E.g. $H_2O$ : central atom O. O has 4 electron pairs: 2 bonded, 2 lone. The shape, including lone electron pairs is Tetrahedral. Ignore the lone pairs now, you will be left with a bent molecular geometry.
Blue is oxygen;
Yellow is hydrogen;
White/Grey are lone/unbonded electron pairs.
I hope this makes sense. :)
If you convert your equation to mol format or another format supported by OpenBabel you can use its tools to add 3D structure information to the files. Also if you need quality conformations you could use tools OpenEye's Omega or as I prefer Balloon which can quickly give biologically significant structures. Balloon works on many different atom types and most smiles Omega is parameterised for a select few smiles.