Notes while viewing the model of (Me₃Si)P(Bu^t)P(Bu^t)P(Bu^t)(SiMe₃)

• All atoms shown at distances and angles that we might expect for a molecule in solution.
• Hydrogens as balls with Van der Waals radius, relative to scale used for bond lengths
• Can see some H's more than just touching:  these control the conformation
• To see skeleton, switch off the hydrogens:

(Right mouse click) Options
Display Hydrogens

Can see contact was between H on Me₃Si and H on Bu^t on next P

• Now for conventional VdW radius model of whole molecule:

(Right mouse click) Options
Display Hydrogens
(Right mouse click) Display
Spacefill
VdW Radii
• Shift left mouse drag to zoom.  Drag down to zoom in, up to zoom out.
• Now looking at a realistic picture of a plastic model which does not actually exist.
• What actually exists is a computer file.  In general, a computer model consists of one or more data files, which are interpreted by programs.

• An .xyz file contains for each atom, its atomic symbol and x,y,z Cartesian coordinates in Angstrom units
• This is the simplest possible format:  it contains no information about which atoms are bonded to which
• A viewer such as Chime contains tables of covalent radii, and works out which atoms are close enough for us to consider as bonded

Chime (or its parent program Rasmol) will read .xyz files directly, but you get default colours

Change to ball and stick

(Right mouse click) Display
Ball and Stick

You also get default ball sizes and a default viewpoint

If you want to put your modelling results on a website, it is best to write a Chime script to tell Chime what to do, so that your model will present its information content as you wish

• Find where in the file I
• specify what .xyz file is to be read in (from the same directory on the website)
• specify the rotation from the default position which I have decided by trial and error to be the best starting view for this lecture
• specify the colours for atoms of various atomic numbers (H 1, C 6, etc.).  The colours are red, green, blue triples, on a scale 0..255
• specify that H is to have a VdW radius of 1.2 Angstroms in the initial view
• If you visit a chime site using an .spt file, you can save the .spt script and the .xyz file it reads.   Right mouse click on the picture;  File then lets you save as an .xyz file or an mdl .mol file (a more complex popular format, used by many modelling and viewing programs).  Right click Edit lets you save the current view to the clipboard as a bitmap for pasting e.g. into Word. To save the .spt script as text (for reading with Notepad), right click on the link to it, in the page from which you accessed it, and select Save link as... .
• For lots of examples of .spt files, you could look at my site  http://www.staff.ncl.ac.uk/bruce.tattershall/teaching/chy277/models.html

(In your other window, return to the original 'Chime rotatable model ..')

• The model consists of xyz coordinates in a computer file, but all distances and angles can be worked out from it
• Most viewers have this ability built into them

• To measure distance using Chime

(Right mouse click) Select
Mouse Click Action
Distance
then click on each of the two atoms.  The distance in Angstroms is reported in a window.
• Try measuring angles instead, by selecting mouse click action angle.

You click on three atoms in turn.  The angle at the middle one is reported