Building Z matrices using Molden
There are three common ways of obtaining a starting
geometry for molecular modelling:
-
Import a previously measured or calculated geometry, e.g. from a crystal
structure
-
Build the molecule using on-screen building facilities in a modelling program
such as Arguslab
-
Create a Z matrix by hand, or using a Z matrix editor such as Molden
-
Method 1 is good if you have access to a previous geometry
-
Method 2 is best for unsymmetric organic molecules
-
Method 3 is good for relatively simple molecules with symmetry, where symmetry
must be retained during geometry optimisation, e.g. because it is known
from spectroscopy that the molecule has this symmetry
-
It is also useful for coordination numbers greater than four, e.g. in octahedral
complexes, which PC modelling programs do not always cope with very well
What is a Z matrix?
-
The most obvious way of specifying a molecular geometry is to give x, y
and z coordinates of each of its atoms, usually in Angstrom units on Cartesian
axes, as in an .xyz
file or a MDL .mol file. The positions of the atoms relative
to each other would be defined with three less coordinates than this,
e.g. by defining one atom to be at position 0,0,0
-
As chemists, we think of molecular geometry in terms of bond lengths, angles,
etc., rather than as atomic coordinates from which such parameters can
be derived
-
The amount of information (i.e. number of numbers required), in the minimum
table of bond lengths, angles, etc. required to define the molecule, is
the same as in a table of Cartesian coordinates such as an .xyz file
-
This minimum table of relationships between atoms is called a Z matrix
-
It is an alternative coordinate system
-
Programs such as Molden or Gaussian can easily calculate Cartesian coordinates
from a Z matrix by elementary three-dimensional trigonometry
-
They can also perform the reverse transformation, but the resulting Z matrix
may not be of much use to a chemist, since the order of the atoms, in specifying
what is connected to what, is critical to whether it can easily be altered,
e.g. to change a substituent
-
If you are going to use Z matrices, it is better to construct them yourself
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]+
-
Before you can do this exercise you must have opened
a signon to unix in the time-sharing computer
aidan, using Secure Shell Client and Exceed. Molden can be used only
with an X-windows server such as Exceed
-
In order to get at Molden easily you must also have set
up your unix id to use BWT's commands. That is assumed in the
following instructions
-
In your xterm window, from your signon directory work, change to
the directory g98, by giving the command
cd g98
-
This is where you will create your own molecular model files in the unix
file system, and keep them for use in a later drylab
-
Give the command
remembering to use only lower case letters
-
A black Molden window and a blue Molden control window full of buttons
open
-
If there is room, pull the black window towards the left of the screen,
and the blue window towards the right, so that they do not overlap
-
It does not matter if they do, but it is less convenient: from the
blue window you can always go to the black window by clicking its title
bar, while from the black window clicking the right mouse button brings
forward the control window and any others that Molden has opened
-
Under Draw Mode, click Solid, Ball
& Stick
-
This will give you balls to click on when you are creating a model:
it is difficult to click on wire models
-
Click Shade
-
This will make balls which are easier to see
-
Click ZMAT Editor.
A blue Zmatrix Editor window with a blank fawn pane within it appears
-
To start, click Add
Line. A Periodic Table appears.
If you wanted a double or triple bond length to the previous atom, you
would now click the appropriate button, before selecting the element, but
this is the first atom, and anyway we will work on the assumption of single
bonds in these species
-
You should model [PCl4]+
first. Always give the central atom first, so click on phosphorus
in the Periodic Table
-
A large purple ball will appear in the black window, and a red P at the
top of the Z matrix pane. This is the atom to which the next atom
will be related
-
Click Add Line again,
and select chlorine
-
You now get a message 'Select 1 Atoms to define the
connectivity of this Center'
-
When you move the mouse cursor over the black window,
it changes to square target, which Molden uses for picking
-
Click on the centre of the phosphorus atom in the
black window
-
You now have a green chlorine ball joined to the
purple phosphorus ball
-
Select the Zmatrix Editor window by clicking on an
unoccupied place of its blue background
-
You now have the second line of the Z matrix, which
shows that Cl is connected to atom 1 (which is P) with a bond length of
2.02 Angstroms, which is a good enough starting guess
-
Add a second chlorine: this time you get the
message 'Select 2 Atoms to define the connectivity of this Center'
-
Click the title bar of the black window to
bring it all into view
-
You need to click first the atom to which the new
chlorine is to be connected, i.e. the purple phosphorus, then the
atom to which a bond angle is to be defined, i.e. the chlorine
-
If your PC has its beep enabled, you should hear
a beep when you pick an atom, but if not, be careful to aim at the centres
of the balls, as you will have no acknowledgement that you have clicked
until it is too late and you have clicked the balls in the wrong order
-
If that happens at any time in these exercises, rub
out the wrong line of the Z matrix by clicking Delete
Line, and repeat adding the atom, before you
go on any further
-
Because you are defining new atoms relative to previous
ones, you must correct mistakes as you go along
-
You now have a bent triatomic molecule
-
The new, third line of the Z matrix shows a bond
length to atom 1 (P) and a bond angle through that atom to atom 2, which
is the first chlorine you added
-
The bond angle defaults to the tetrahedral angle,
which happens to be what you need for this geometry
-
For the next chlorine atom you add, you will be asked
to select three atoms
-
In the remaining exercises, some thought is needed
about strategy at this point, but here we can do the obvious
-
Select P as the first atom again
-
For the second atom, use the same chlorine as last
time, i.e. the one horizontally situated relative to the phosphorus, since
the second, third and fourth chlorine atoms all have the same angle to
the first one
-
A fawn line is drawn along the P-Cl bond
-
The third atom to be selected is one to which a dihedral
angle is to be defined
-
Click on the other chlorine atom
-
In the new, fourth line of the Z matrix, the final
columns have been filled in, showing a dihedral angle of 1200
to atom 3, which is the second chlorine you added
-
This also is conveniently correct for a tetrahedron
-
To illustrate what this means, which you must understand
before you can proceed, right click on the black background of the
model window, to raise the Molden Control window
-
Click the Dihedral
button
-
In the white pane at the bottom of the Molden Control
window, you get the message 'Click on four atoms !'
-
In the black, model window, select the atoms in the
same order as implied by the line of the Z matrix, i.e. click the new chlorine
atom (sticking towards you) first (since that is the atom whose Z matrix
line it is), then the phosphorus
-
The fawn indicator lines must be drawn as you go
along, otherwise you have not succeeded in clicking on the centres of the
balls
The third atom to select is the bond angle chlorine
(horizontal), and the fourth atom is the dihedral atom chlorine (pointing
upwards)
-
The three fawn indicator lines, with the last one
going through space between the two ligands, describe a very distorted
letter Z, which is why this system of coordinates is called a Z matrix
-
So that you can see it better, you are going to turn
the model so that you look down the middle, connecting line of this Z,
i.e. from the 'bond distance atom' P to the 'bond angle atom' Cl
-
First click on the black spot at the bottom right
of the controls window
-
This causes sticky mouse pointer rotation
-
(Anywhere) in the black model window, carefully left
drag horizontally to the right, until the 'bond angle chlorine' disappears
completely behind the phosphorus
-
You are now looking down the centre line of the Z
-
You see the bond to the new chlorine atom (at the
bottom of the window) and the bond to the 'dihedral atom chlorine' (at
the top of the window) both as projections on a plane perpendicular to
the centre line of the Z (from the 'bond distance atom' P to the 'bond
angle atom' Cl)
-
You see that to go from the projection of the bond
to the new atom, to the projection of the bond to the 'dihedral atom',
you need to turn your head clockwise by 1200
-
The entry in the Dihedral column of the Z matrix
is (+)120.0
-
When you have finished constructing your tetrahedron,
the view you are now looking at will be down a three-fold axis, so you
knew already that the dihedral angle should be 1200
-
Restore the original view by left dragging until
the 'bond angle chlorine' is back on the left side of the window
-
The bottom chlorine should still have a red circle
around it, because that is still the current atom in the Z matrix
-
Add the fourth chlorine in exactly the same way as
the previous, third chlorine, i.e. use the horizontal chlorine as the bond
angle atom, and the top chlorine as the dihedral angle atom
-
This is a clearer way of doing it than using the
previous chlorine as the dihedral angle atom
-
The fourth ligand appears at the back of the model
-
The dihedral angle in the last line of the Z matrix
is shown as 2400, which is the same as -1200
-
Try clicking this dihedral angle box in the Z matrix,
and backspace to completely delete the number. Type in -1200
and
click Apply Changes to current Z-Mat
Nothing should happen to the appearance of the model
-
A negative dihedral angle means an anticlockwise
rotation relative to the bond to the dihedral angle atom
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
-
First save the model as a simple .xyz file of Cartesian coordinates, which
Molden will create for you
-
At the bottom of the Zmatrix Editor window, click the Cartesian
button, then XYZ
-
In the 'File name ?' box, type pcl4.xyz then
click Write Z-Matrix
-
A 'Successfully wrote file:' message appears
-
You can look at the file you have just written, as
follows
-
In another xterm window (if you created only one
when you signed on, create another now by xterm & in your Secure
Shell Client window) cd to g98 and enter dir
-
You should see a directory listing including your
file pcl4.xyz
-
Give the command more pcl4.xyz, in which you
can pick up the name of the file from the directory listing by X-windows
copy and paste, which you should practice
-
You will see that phosphorus, atom 1 in your Z matrix,
has been given the coordinates 0,0,0
-
The first Cl differs only in z coordinate, so it
lies along the z axis
-
The second Cl lies in the xz plane, and the other
two are symmetrically on each side of it, with equal but opposite y coordinates
-
Next you will save the model as a Z matrix
-
Leave the second xterm window open and select the
Molden Zmatrix Editor window
-
Click the Gaussian
button at the bottom of the window
-
Alter the file name to pcl4.com, which has
the file name extension for command files for Gaussian
-
Click Write Z-Matrix
-
Give the command more pcl4.com in your spare
xterm window
-
You will see a Z matrix just like the one in Molden,
but with variable names instead of bond lengths, angles, or dihedral angles
-
Underneath the Z matrix is a list of these variables
and the numeric values they have at present
-
This is all ready for a modelling program to change
the values as it optimises the geometry
-
Next you will fix the symmetry of the species (so
that an unsophisticated modelling program will not change it)
-
Go back to the Molden Zmatrix Editor window
-
For a regular tetrahedron, you need to fix all the
angles as constant, and make all the bond lengths be variable but tied
together so that they always have the same value
-
This is done by using the same variable name for
all the bond lengths in the written-out Z matrix, and using actual numbers
rather than variable names for all the constants in the Z matrix
-
You need to use the simulation of a unix mouse middle
button for this. On a simple two-button mouse, this is pressing both
buttons at once, while on a wheel mouse it may be pushing the wheel inwards.
Whichever it is, do it to to the bond length box for the second chlorine
(atom 3) in the Z matrix
-
A dropdown menu appears: left click on link
-
A message 'Click on a Z-matrix Bondlength' appears
(further down the window)
-
Left click on the bond length for the first chlorine
(atom 2). The linked bond length turns yellow to show that it is
now dependent
-
Repeat the process for the other two chlorine bond
lengths
-
After this, only the first chlorine bond length should
be independently variable (grey background)
-
Now treat all the bond angles and dihedral angles
similarly, but select constant
instead of link
from the dropdown list
-
No further click is required, and the angle box turns
green to show that it is a happily fixed constant
-
In the end, the only variable (grey background) left
in the whole Z matrix should be the one bond length
-
Now click Write Z-matrix to overwrite your previous
file pcl4.com
-
Look at its contents again in the spare xterm window
-
Now you will see that there is only the one variable
below the matrix for the modelling program to optimise
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.
-
However distorting your eyesight, a Z must have two bends in it, otherwise
it is not a Z
-
In other words, you cannot define a dihedral angle if either of the two
bond angles connecting the four atoms is 1800, because the projection
of one of the end bonds would be a point, not a line to which a dihedral
angle could be defined
-
This is a problem which occurs for linear groups such as azide or terminal
carbonyl, or in linear arrangements within higher symmetry systems such
as trigonal bipyramidal or octahedral
-
For the bigger coordination numbers, the solution is simple: you
just have to define the atoms in an order such that they can all be at
a non-linear angle to a previously defined pair
-
For the trigonal bipyramid, if you add one of the apical ligands first,
and try to define the other ligands relative to it, you will get stuck
when you come to the other apical ligand trans to it
-
If you start with one of the equatorial ligands, none of the remaining
ligands is trans to it, so there is no problem
-
It is easiest here to start the model from nothing, rather than modify
the previous one, so click New Z-mat,
which rubs out the old one
-
Add phosphorus and the first two chlorine atoms to
produce the bent triatomic molecule as before
-
Now edit the bond angle from the default tetrahedral
angle, to 1200, the equatorial angle in a trigonal bipyramid
-
Click Apply Changes
to current Z-Mat
-
Now add the third equatorial chlorine
-
Molden sets its bond angle to 1200, the
same as the previous
-
It knows about trigonal planar species, so it sets
the dihedral angle to 1800, in other words, the angle about
one of the three two-fold axes
-
What would happen if you set the dihedral angle to
00? Try it, then set it back to 1800
-
Now add the first apical chlorine, defining it relative
to the first two chlorines as before
-
Alter the bond angle to 900
-
Whoops! Something a bit non chemical has happened
to the model! You have a strong bond between the new chlorine and
one of the others, when really there should only have been Van der Waals
interaction
-
Clearly, the dihedral angle is wrong, and is causing
the atoms to be closer than the sum of their covalent radii, so Molden
thinks they should be displayed as bonded
-
Like an .xyz file, the data within Molden does not
contain bond information: it decides what to display as bonded and
what not, purely from interatomic distances, as it goes along
-
What it labels as BondLength in its Zmatrix Editor
window may not be the length of a chemical bond: it is just the distance
between the two atoms. However, when, as now, you add lines to a
Z matrix, it sets the default distance appropriately for a bond between
the two elements
-
What should the dihedral angle be?
-
If in doubt, left click on the dihedral angle in
the Z matrix, then turn the model so that the green ringed (a bit hard
to see against the green ball!) 'bond angle' chlorine is at the back
-
The red ringed chlorine is the new one
-
What should its dihedral angle be to the blue ringed
'dihedral angle' chlorine?
-
Set the dihedral angle to this value and click Apply
Changes to current Z-Mat
-
Add the other apical ligand in the same way, setting
the bond angle to the first equatorial chlorine to 900
-
What should the dihedral angle be this time, to make
the final apical chlorine come out trans to the first?
-
Do it
-
Save the Cartesian XYZ file as pcl5.xyz, as
before, remembering to change the output format as well the file name before
clicking Write Z-Matrix
-
To set the symmetry, again all the angles are known
constants, so make them green as before
-
There are now two different bond lengths, one for
equatorial ligands and one for apical ligands
-
They are all the same at present, because Molden
does not know about trigonal bipyramids, but they will not be after optimisation
by Gaussian
-
Link the second and third equatorial chlorine bond
lengths (atoms 3 and 4) to the first (atom 2), and the second apical bond
length (atom 6) to the first (atom 5)
-
You should have two bond lengths left on grey backgrounds
-
Change the apical bond length to a bit longer, e.g.
2.2, and click Apply Changes to current Z-Mat
-
The linked bond length changes automatically to follow
the variable one
-
The reason for making this adjustment is so that
Gaussian does not think you meant the two kinds of bond lengths to stay
equal, even though you did not assign them to the same variable.
Modelling programs can get too clever sometimes in trying to read your
mind
-
Change to Gaussian output format and write the Z
matrix as pcl5.com
A model of [PCl6]-
-
Do this in the same way as for the trigonal bipyramid
-
Think of the first ligand you add as defining an axis, and the next four
ligands as being equatorial about that axis, so they all have 900
bond angles to the first, and various dihedral angles to each other
-
The real difficulty is, that because of the symmetry
of the system, the ligands keep getting in the way when you need to click
three atoms in adding the next one
-
You just have to keep turning the molecule round
-
It will be easier to see if you make it smaller by
zooming out using the Out
button on the control panel, and setting shading on using the Shade button
-
Click on the last dihedral angle done in the Zmatrix
Editor window, so as to label the balls with coloured rings
-
Remember that the second atom to click, after phosphorus,
is the green ringed ball, and the third atom is the blue ringed ball
-
Rotate the molecule so that you can see the centres
of all three of these balls, before you click on Add
Line. Once you are into the Add Line
conversation, you can no longer rotate the molecule, which is a deficiency
of this version of Molden
-
If you get stuck in this way, just add the atom to
anywhere in the molecule, and then remove it with Delete
Line
-
Note that you cannot add the final, axial ligand
in the same way: to avoid the 1800 bond angle,
you must chose one of the 'equatorial' ligands, e.g. atom 3, to define
the bond angle to
-
Then you can define the dihedral angle as back to the first chlorine (atom
2), when it will be 1800
-
As for the tetrahedral case, make all the angles constant and link the
last five bond lengths to chlorine to the first
-
Save in Cartesian XYZ and Gaussian formats, as pcl6.xyz and pcl6.com
respectively
-
Exit from Molden by clicking the Skull and Crossbones
button, OK
Remember that to log off from unix, you enter exit
in each xterm window, to close it, then exit in the Secure Shell
Client window. Finally close the Secure Shell Client window.