Example 2 TH1
(It is best to look at the JH21 example first if you are not familar with ORTEX)
start Oscail select TH1 and run ORTEX the view in ATOM mode is
The nitrogen of the acetonitrile is N3 and this will bond to the Ni if the covalent bond tol. is raised in ORTEX setup to 0.3. A search for contacts around the coordinated water O5 shows a H-bond to the isolated chloride (3.061).
Distances from O5 ( 4,55501) to atoms 1 through 33
O5 ( 4,55501) 0.9177 0.3901 0.7002
Ni1 1 0.7714 0.4541 0.6640 11. .05 !( 1,55501) D = 2.072
O2 1 0.8052 0.4512 0.5639 11. .05 !( 7,55501) D = 2.859
O1 1 0.7354 0.2533 0.6330 11. .05 !( 12,55501) D = 2.893
N1 1 0.7283 0.4190 0.7588 11. .05 !( 9,55501) D = 2.932
N2 1 0.8063 0.6581 0.6777 11. .05 !( 11,55501) D = 2.947
Cl2 1 1.0501 0.5690 0.8112 11. .05 !( 3,75604) D = 3.061 H-B
Putting in the increased covalent bond tol. and Type 2 H-bonds (atom range Cl2 to O5) gives
Select Extend Lattice Using Bonds / H-Bonds and set the atom range to Cl2 to O5
Adding several units gives.
At any stage during the addition of units selecting NO will return to the display and allow rotation of the structure. Extension may then be resumed.