The "oxidation state" parameter assumes the opposite extreme, that the atoms are totally ionic. Electrons are assigned to the most electronegative atom. This can be changed manually in the Properties Explorer. Oxidation state affects the ionic radius of the atom in Materials Studio.

Hybridization describes the geometry of the bond, and matters for Discover energy calculations and simulations. There are a number of hybridization types with corresponding force fields, for example, in the Discover setup and they refer to specific bonds. For example the hydrogen-nitrogen bonds in the ammonia molecules are called "h1n" and the nitrogen electron arrangement is "n3*". In the ammonium ion the bond types change to "h1+" and "n4+". These can be typed automatically by the program or set manually.

On the other hand orbitals can be calculated, using density functional theory / LDA approximation, with the DMol3 module. For this you set the total charge on the molecule. The code handles delocalized electrons and calculates the total energy of the system.

Temperature factors and diffraction

Temperature factors can be part of a structure specification (when crystal building or reading a structure file), a refinement (using the Reflex module), or can be entered by hand in Properties Explorer. The Visualizer will display thermal ellipsoids, but you need to explicitly add them to the representation: the dialog for the settings is in View -> Display Style -> Temperature factors. The thermal parameters affect how diffraction is calculated. The figures below show the CdTe lattice without and with thermal ellipsoids added. In the latter case the (420) peak is brought up strongly. Note there's no effect on the peak width. Peak broadening is modelled for small crystal sizes however, in the Reflex setup.

The reason we were playing with the CdTe lattice was in order to model Zn sitting on Cd sites as static (not averaged) disorder, and model the resulting changes to the lattice in diffraction. Building the model is straightforward. Unfortunately it turns out not to be effective using Discover (force field model) to try to relax the lattice around the Zn sites: the electronic states aren't handled properly. The ab initio method (DMol3) would work. Once the lattice is relaxed, Reflex can be used to calculate diffraction.

Tables of bond lengths and angles

The easiest way to obtain particular bond lengths and angles is to use the Visualizer directly, which has tools for this. To make tables of all the position information, export the data in ascii format: File -> Export -> InsightII format. This writes files *.car and *.mdf which contain ascii text tables of the atoms positions. Here they are for ammonia. The first file has the x,y,z positions of the atoms. The second file specifies connections between atoms.

!BIOSYM archive 3 
PBC=OFF 
Materials Studio Generated CAR File 
!DATE Tue Jul 15 09:38:47 2003 
N1 -1.034796723 0.640566743 -0.479686745 XXXX 1 n3* N -1.059 
H1 -1.404713550 0.117291141 -1.386021676 XXXX 1 h1n H 0.353 
H2 -1.404534696 1.687177319 -0.479897659 XXXX 1 h1n H 0.353 
H3 0.075203660 0.640288699 -0.479417807 XXXX 1 h1n H 0.353 
end 
end

!BIOSYM molecular_data 4
 
!Date: Tue Jul 15 09:38:47 2003   Materials Studio Generated MDF file
 
#topology

@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
 
@molecule Sketch2
 
XXXX_1:N1           N  n3*     ?     0  0    -1.0590 0 0 8 1.0000  0.0000 H1 H2 H3 
XXXX_1:H1           H  h1n     ?     0  0     0.3530 0 0 8 1.0000  0.0000 N1 
XXXX_1:H2           H  h1n     ?     0  0     0.3530 0 0 8 1.0000  0.0000 N1 
XXXX_1:H3           H  h1n     ?     0  0     0.3530 0 0 8 1.0000  0.0000 N1 
 
#end