MOLDEN

 

Molden is a program for creating input data for Gaussian (a Quantum Mechanics

program). It can also be used for viewing the results of a Gaussian calculation.

It should always be used to view the results of a calculation as it confirms the

right geometry was used for input and a sensible geometry was produced at the end of the run.

 

To View Results.

 

To view the results of a Gaussian run (where the output is written to benzene.out)

type:

 

    molden benzene.out

 

(Obviously if your output file is called something else use that file name).

 

Once molden has produced a picture of your molecule and the control panel for

program, check the geometry being displayed is sensible. When you have done this

click on the button labelled movie.  This will show you how your molecule has

changed under geometry optimisation. When the molecule has stopped moving, check

the geometry is sensible. Do not assume that the Gaussian Program will produce

sensible structures. You may feed in a wrong geometry to begin with and

end up with a structure you were not expecting.

 

You can find out bond lengths, bond angles and dihedral angles by clicking on

the appropriate box in the control panel and then clicking on the the relevant

atoms in the picture.

 

 

Building a Z-matrix

 

What is a Z-matrix?

 

A z-matrix is just a way of specifying the geometry of a molecule. Most

programs use cartesian coordinates for molecular geometry, but we tend to think

in terms of bond lengths, bond angles and dihedral angles, so we need a way

defining the positions of atoms in a molecule in terms of our commonly accepted

concepts.  Below is an example of the z-matrix for methane,

 

  C

  H  1  1.09

  H  1  1.09 2 109.5

  H  1  1.09 2 109.5 3 120.0

  H  1  1.09 2 109.5 3 -120.0

 

The explanation of the above z-matrix is as follows. The first line is 'C'. This

means atom number one is a carbon atom.  The second line is 'H  1  1.09'.

This means the second atom is hydrogen and it is bonded to atom one with a bond

length of 1.09 Angstroms. This forms the first C-H bond.  The third line is '

'H  1  1.09  2  109.5'. This means hydrogen is bonded to atom one at a distance

of 1.09 Angstroms and positioned such that it makes an angle of 109.5 degrees

with atom number two (i.e. the H-C-H angle is 109.5 degrees). The forth line is

'H  1  1.09 2 109.5 3 120.0' and means a hydrogen atom is bonded to atom one

at a distance of 1.09 Angstroms, such that it makes an angle with atom 2 of

109.5 degrees and a dihedral angle of 120.0 degrees with atom 3. The fifth

line is similar except the dihedral angle is -120.0 degrees (if it was 120.0

and not -120.0 degrees it would lie on top of atom 4).

 

 

To build Methane with Molden

 

Type 'molden' and press the return key to get molden running.

Once molden is running click on 'ZMAT Editor' button.

A new window appears. Click on 'Add line' in this new window.

A periodic table appears, click on carbon. This puts a carbon atom ion the

molecular viewer window and a C in the z-matrix editor box.

Now click on 'Add line' again. Note you get the periodic table again and below

it the choice of bond type. Leave the default bond type at single and click on

H in the periodic table. Now click on the carbon atom in the molecular viewer

window. This tells the program what atom to bond this new hydrogen to.

Now click on 'Add line' again. Choose single bond (default) and click on H, now

click on C in the molecular viewer window and now click on H in the molecular

viewer window. Clicking on carbon tells the program to bond this new atom to

carbon and clicking on hydrogen second tells the program to make an angle with

hydrogen. Again click on 'Add line' . As before choose hydrogen and click on

C then one hydrogen and then the next hydrogen. This tells the program to bond

this hydrogen to carbon and then make angle with the first hydrogen clicked on

and a dihedral angle with the next hydrogen clicked on. Finally, add the last

hydrogen, click on 'Add line' and as before choose a single bond (default) and

click on hydrogen. The go to the molecular viewing window and click on C and

one of the hydrogen and then another hydrogen. This should give you methane.

By the words 'File name ?' there is a box. Put the name of the molecule in this

box. If you have a file with this name already choose another name. Now click

on the button 'Write Z-Matrix'. If you now look in your filestore you should

see the file with the z-matrix in it. It will be in a slightly different form

to the example given above, as the bond lengths, angles and dihedral angles

are assigned symbolic values (i.e names rather than values) and the names are

given values below.

 

This example should enable you to build a z-matrix for the molecules of

interest to you.  Note that you can add groups to the z-matrix with one of the

buttons.  In addition, you can alter the values assigned to a bond length or angle by

clicking on the box that has the relevant bond length or angle in it, deleting

what is there and typing in a new value.