Building Z matrices using Molden

There are three common ways of obtaining a starting geometry for molecular modelling:
  1. Import a previously measured or calculated geometry, e.g. from a crystal structure
  2. Build the molecule using on-screen building facilities in a modelling program such as Arguslab
  3. Create a Z matrix by hand, or using a Z matrix editor such as Molden

What is a Z matrix?

Models of PCl5 and its derivatives

In this exercise, you will construct starting geometries for tetrahedral [PCl4]+, trigonal bipyramidal PCl5, and octahedral [PCl6]-.  These are chosen as the simplest common examples of related species in all three major geometries, which can be modelled by the pm3 method.  In future exercises, you will optimise the geometries and calculate modes of vibration for them

Using Molden to construct [PCl4]+

Saving and Symmetry

Now you have a model (though not an optimised one yet) of [PCl4]+.  Your next job is to save it for later

A model of PCl5

This molecule, with trigonal bipyramidal symmetry, is known in the gas phase, though the solid is [PCl4]+[PCl6]-.  Besides having to type in some angles yourself, the difference of this case from that of [PCl4]+ is that one of the angles, between the two apical (axial) bonds, is 1800.

A model of [PCl6]-

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