Ionic Organic Crystal Structure Prediction using Ritmol
Described in
A method for the
prediction of the crystal structure of ionic organic compounds—the crystal
structures of o-toluidinium chloride and bromide and polymorphism of
bicifadine hydrochloride
Patrick McArdle,
Karen Gilligan,
Desmond Cunningham, Rex Dark, Mary Mahon, CrystEngComm, 2004, 6,
303.
Demonstration run using the otolcl4 job, o-toluidinium chloride, which
is included with the ritmol download
Before you can follow this tutorial on your PC you must have installed Oscail, Moilin and
Ritmol (in that order).
There are three steps in the procedure:
1 Building the model and generating the ion pair packs using Moilin.
2 Generating and refining the 29 Molpak packs using Ritmol.
3 Running Powcomp to compare the observed powder pattern with the predicted patterns.
The files for starting at step 2 are supplied and this is the best place to start.
.....Starting at step 2
The reference powder pattern is processed first
Run Oscail use the open file dialog button 
with the
Files of type filter set to Powder File .ING to navigate to \shelx\ritmol\ select
OTOLCV.ING and click Open. The Oscail status bar should now have otolclv and
\shelx\ritmol as Jobname and Current Directory respectively.
Click the Powdis button 
select Label / Label All Peaks and set Noise Level (counts) to 90. Close
Powdis and Oscail will return.
Starting Ritmol and generating Molpak input
Use the open file dialog button ,
with the Files of type filter set to
Moilin file XYZ, to navigate to \shelx\ritmol\otolcl\ select OTOLCL4.XYZ and click
Open. The Oscail status bar should now have otolcl4 and \shelx\ritmol\otolcl as Jobname and Current Directory respectively.
Click the Run job button 
and on the Roinn 2 Tab select
Ritmol and OK.
On the Ritmol Menu click Setup and check Select All and OK. Click Moilin2Mol and XYZ converted to Molpak should appear 6 times.
This converts Moilin xyz files to Molpak input files and six sub folders are also generated.
Click DirsFiles and wait until Calculating is replaced by Idle
on the status bar. This action will generate 29 subfolders of each of the 6 subfolders generated in the last step these are (AA, AB, AC etc. which Molpak users will recognize)
Click Setup for this demonstration and to speed things up select only
XP and AY and click OK (It would be normal to select ALL and OK).
All should now be ready for the Molpak/WMIN run.
Running Molpak / WMIN
Click RunMolpak and 25 Molpack steps with WMIN optimization will be run for the
XP/AY pack.
When the status bar is back to Idle you can click Edit.LOG to
see how much time was used.
To generate summary tables click Ch.DIR and select the XP
folder in \shelx\ritmol\otolcl and click OK.
Click Summary this will generate tables which can be examined in Excel
etc. if XM, YP etc. had been selected for the RunMOL1 command then Summary
should also be run on these packs. When the Molpak / WMIN run is finished you
can stop Processkiller.
.....Step 3
Powcomp run
Use Ch.DIR to select \shelx\ritmol\otolcl and click OK. Click Powcomp and on the
dialog select click OK. When the
open file dialog appears with "Find REFERENCE LST file" in the title
bar you will need to find the file generated by
Powdis above. Nnavigate to \shelx\ritmol\ where you should find
otolcv.lst select it and click OK. When Powcomp has finished you
can examine the results in the log file using EditPowcomp.LOG function on the menu. The top of the file should look like the following; (A copy of the log file is in the reference pattern folder, ritmol_powcomp.log)
Powcomp Run
Time/Date 18:20: 6 17/ 2/2006
Ref name otolcv.LST
Ref path C:\shelx\ritmol\otolcl
AngTol NMF SAF T4M MinC BSep Btres Berr DSPACE
0.30 0.33 0.25 2 4000 2.80 10000 2.50 7.00
***********************************************
Reference Band Analysis
Bno. Start End Max.pk Max.cnt Tot.cnt Pk.no.
Band 1 15.05 19.95 15.05 37493. 135941. 5.
Band 2 23.25 35.05 26.80 99000. 488261. 12.
Sample Analysis
pack name Rno. Sno. M1 M2 BMATCH T4R+S RNM RNM4 BN
XP AA topden_ 17 10 0.0208 0.0000 0.500 2. 12. 2. 2
XP AB topden_ 17 14 0.0029 0.0000 0.000 0. 14. 3. 2
XP CA topden_ 17 21 0.0048 0.0048 1.000 0. 12. 0. 3
XP AH topden_ 17 7 0.0010 0.0000 1.000 0. 15. 4. 3
XP AI topden_ 17 19 0.0137 0.0137 0.000 0. 8. 1. 2
XP AK topden_ 17 28 0.1071 0.0000 0.500 0. 5. 1. 5
XP AM topden_ 17 6 0.0008 0.0000 0.500 0. 15. 4. 1
XP FA topden_ 17 2 0.0000 0.0000 0.000 0. 17. 4. 1
XP DA topden_ 17 4 0.0003 0.0000 0.000 0. 16. 4. 1
XP DB topden_ 17 4 0.0000 0.0000 0.000 0. 17. 4. 1
XP DC topden_ 17 8 0.0011 0.0000 0.000 0. 15. 4. 1
XP DD topden_ 17 11 0.0008 0.0000 0.000 0. 16. 4. 2
XP DE topden_ 17 6 0.0004 0.0000 0.000 0. 16. 4. 1
XP BA topden_ 17 20 0.0060 0.0060 1.000 1. 11. 2. 4
XP BB topden_ 17 18 0.0144 0.0000 0.000 1. 8. 3. 3
XP AZ topden_ 17 14 0.0029 0.0000 0.500 0. 14. 3. 3
XP AY topden_ 17 19 0.6842 0.6842 1.000 2. 5. 0. 2
XP BH topden_ 17 3 0.0002 0.0000 0.000 0. 16. 4. 1
XP AV topden_ 17 9 0.0019 0.0000 1.000 1. 15. 3. 3
XP BD topden_ 17 7 0.0000 0.0000 0.500 0. 17. 4. 1
XP BF topden_ 17 7 0.0005 0.0000 0.500 0. 16. 4. 1
XP CC topden_ 17 5 0.0003 0.0000 0.000 0. 16. 4. 1
XP CB topden_ 17 5 0.0003 0.0000 0.000 0. 16. 4. 1
XP CD topden_ 17 10 0.0014 0.0000 0.500 0. 15. 4. 2
The XP AY pack has been selected as it has the best Match index.
The quantities listed in the table are;
Rno. Number of peaks in reference
Sno. Number of peaks in sample
M1 Initial match
M2 match modified by subtracted area fraction
BMATCH Band analysis match
T4R+S Number of peaks in top 4 of reference and sample
RNM Number of reference peaks not matched in sample
RNM4 Number of peaks in reference top 4 not matched
BN the number of bands detected in the sample pattern
.....Starting at step 1
Generating the ion pair packs
Copy the files otolcl4.XYZ, counter.XYZ and otolcl4_chg.log to the empty
\shelx\ritmol\test folder (If it is not empty delete all the files and
subfolders it contains before you copy the files).
Run Oscail use the open file dialog button
with the
Files of type filter set to Moilin File .XYZ to navigate to
\shelx\ritmol\test select otolcl4.XYZ and click Open. The status bar should now have otolcl4 and
\shelx\ritmol\test as Jobname and Current Directory. Use 
to start Moilin-X. DO NOT ROTATE STRUCTURE. On the Moilin-X toolbar click 
to start Moilin-9. On the Moilin-9 toolbar click to go into build mode 
,
click 
to set the
origin atom and then click the centre of the blue nitrogen. Click Counter on the
Moilin-9 menu and the six ion pair packs are generated. The six packs generated
are in the files otolcl4XP.XYZ, otolcl4XM.XYZ etc. These ion pairs can be
examined using Moilin. In some of them the counter ion and the target atom may
be far apart. However, remember that when the ion pairs are packed this may not
be the case. You could now continue
at Step 2 above.
Generating the ions and computing atom
charges
The files to be generated are jobname.XYZ, counter.XYZ and jobname_chg.log
Build the largest ion (the cation in this case) using Moilin and optimize
the structure using dft B3LYP and a 6-31G* basis set using either Gaussian or
Gamess. Save the file under a suitable jobname (this will generate jobname.XYZ
which in this case is otolcl4.XYZ).
If the smaller ion is also multi atom you will need to do the same for it and
save it using the name counter (You will then have a coordinate file
called counter.XYZ) . In the present case the counter.XYZ file is trivial
but is still required you can generate it by saving the jobname.XYZ as
counter.XYZ and deleting all but the first two lines and editing it to give.
1 otolcl4
1 CL 0.000000 0.000000 0.000000 15
The 15 is the atom type in general these are MM3 atom
types which are listed in the Moilin/Tinker/help however it is what appears in
the text file typcon.dat that is important.The file typcon.dat is in
\exe
and in that file Cl is type 15. You can edit and change typcon.dat but be
careful.
Atom charges: The atom charges file
written GAMESS under Moilin is called jobname_chg.log. If you use another program the atom charges can be found in the listing file of the program you use and a text editor can be used to produce a file which looks like the following one produce under Moilin.
#GAMESS
C 0.085178
C 0.154513
C -0.205002
C -0.050141
C -0.040090
C -0.152940
H 0.158903
H 0.133333
H 0.128730
H 0.149204
C -0.243654
H 0.082317
H 0.130765
H 0.082063
N -0.543190
H 0.374217
H 0.374560
H 0.381235
Cl -1.000000
When an anion and cation are put together it is necessary to put the atom charges for both ions into one file this can be done using a text editor.
In the present simple case
the charge for Cl has been typed in at the end and the file is otolcl4_chg.log.
Back