CCP14 Homepage - Single Crystal and Powder Diffraction - Methods, Problems and Solutions - Powder Diffraction Structure Solution Pathways - Solving an Organic Structure (Cimetidine) from Powder Diffraction Data - Initial Connectivity Searching using the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD

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Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

Solving an Organic Structure (Cimetidine - C 10 H 16 N6 S) from Powder Diffraction Data

Initial Connectivity Searching using the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD

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This example uses example Cimetidine data from the EXPO software

Zip file containing the Cimetidine data and various input files.

Before doing anything with the data (peak profiling, powder indexing, etc), it might be a good idea to see if it may already have been solved; and/or what related structures may exist and look like. Thus we will use the expected molecular connectivity to find out what related structures have already been solved.

Go to the CORINA page at http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html and scroll down until you see the data entry for the SMILES string.

Corina web interface

Select the Create Molecule button to bring up the JME Molecular Editor and enter the fragment in 2D format. You may like to play with just entering a part of the structure - or the entire structure - and see what the optimisation algoirthm does. Here we have entered the entire molecule.

JME Molecular Editor

Now Submit the fragment to be minimized into a 3D conformation; and viewed with the JAVA applet (smile string it uses being CNC(=NC#N)NCCSCc1nc[NH]c1C).

JME Molecular Editor

Save the now 3D fragment into PDB file ready to import into various crystallographic software. In this case, directly import into Platon to use it's ability to generate Quest scripts.

(Note: Ortep-3 by Louis Farrugia can import a PDB file and save it as a Shelx file in a ready to edit format.)

Now it is time to check out the fragment in the Cambridge Database, using Platon as a user-friendly interface.

If you are already running Platon on a UNIX computer where the CSD and Quest already been installed, this is extremely trivial.

In this example we will deal with the case where the user is on a Windows PC, and the CSD database is on a remote UNIX machine where Platon has been compiled. (it is possible to generate the Quest query on Platon for Windows and ftp it over to run manually in quest - using a command line similar to quest -j structure_name < structure_name.que)

NOTE: With quest, make sure it is not automatically going into Xterm/Menu mode or the following will not work. By default, Quest should not go into Xterm/Menu mode but the administrator may have set it up like this to save on a few keystrokes.

If you have not done already, information on settup up for Secure FTP and Secure X sessions from a Windows machine, refer:

Secure MS-Windows to UNIX machines based X-Sessions via Secure Shell Tunnelling (Using Teraterm for Windows and MI/XServer v 5.6 as an example)
Secure FTP transfers via Secure Shell Tunnelling (Using Teraterm for Windows and WS_FTP as an example)

If a UK based academic or student, you can obtain free and easy access to the Cambridge and other structure databases via the EPSRC funded CDS - Chemical Database Service (free registration is done On-line)

FTP the PDB file to the remote machine. In this case the Chemical Database Service server (freely available after registration for any UK based academic or student) at cds.dl.ac.uk. (you will need your CDS username and password handy to do this)

Run teraterm and login to the UNIX computer containing the Cambridge database (in this case cds.dl.ac.uk).

Run your Windows X-server (in this case the MI/XServer for Windows)

In the teraterm shell, go to the directory where the Shelx INS file with the starting information is, then type platon cime.pdb. This will spawn the following window in your windows X-server.

Running a UNIX Platon via a Windows X-server

To redraw a screen if you swapped into a Window program, just use CONTROL L.

Following is how the structure looks in Platon using Pluton, then ADP (ORTEP) mode. (Just use the options under Graphics to do this).

Viewing the structure in Pluton mode

Under the REPORT option, select CSD-QUEST and Platon will generate the Quest file then try and spawn Quest if this is available locally. If you swap into the Teraterm screen, you can see Quest running finding hits!

Searching the Cambridge Database via Platon Spawning a command line Quest session

Platon will now display the structures that were found graphically.

As this shows that Cimetidine has already been solved, doing this first could save you a lot of bother.

In the present April 10th version of Platon, use the bottom right PREV and NEXT menu option to go to the next structure if it found more than one. This can include structures with interesting co-ordination with metals.

Platon graphically presents the results from the structure search on the screen

If platon tells you it got hits (on the bottom left of the screen) but does not give display a structure, but gives the following output at the bottom right of the screen. It could be there is a nuance with Platon and the Windows X-server in being able to spawn extra screens. Look manually in the Quest files, and these will tell you want structures it found.

Even if things go well, you can of course view manually the jnl journal file.

You can do the following manually in Quest by copying the *.QUE Quest file generated by Platon to a machine with Quest on it and run quest and import the file.

quest -j structure_name < structure_name.que

QUEST Query file

SAVE 3
T1 *CONNSER
AT1  C     1
AT2  N     2
AT3  C     3
AT4  N     2
AT5  C     2
AT6  N     1
AT7  N     2
AT8  C     2
AT9  C     2
AT10  S     2
AT11  C     2
AT12  C     3
AT13  N     2
AT14  C     2
AT15  N     2
AT16  C     3
AT17  C     1
BO     1     2 99
BO     2     3 99
BO     3     4 99
BO     3     7 99
BO     4     5 99
BO     5     6 99
BO     7     8 99
BO     8     9 99
BO     9    10 99
BO    10    11 99
BO    11    12 99
BO    12    13 99
BO    12    16 99
BO    13    14 99
BO    14    15 99
BO    15    16 99
BO    16    17 99
END
QUESTION T1

The Resulting Journal File

COMM +----------------------------------------------------------------------+
COMM | These are comments in the QUEST initialisation file. This file can   |
COMM | contain QUEST commands, such as terminal type, that are always read. |
COMM | For more information enter "HELP INITIALISATION FILES" within QUEST. |
COMM +----------------------------------------------------------------------+
COMM | For more information on...                                           |
COMM |    the database of CSDS citations,      type "HELP DBUSE"            |
COMM |    starting the graphical interface,    type "HELP GRAPHICS"         |
COMM |    the distributed release notes,       type "HELP RELEASE NOTES"    |
COMM |    the PreQuest data input program,     type "HELP PREQUEST"         |
COMM |    the CIF/MIF output file,             type "HELP SAVE"             |
COMM +----------------------------------------------------------------------+
COMM | Visit the CCDC web site at:             http://www.ccdc.cam.ac.uk/   |
COMM +----------------------------------------------------------------------+
COMM  Set better PRINT style:
      PRINT 10
COMM +----------------------------------------------------------------------+
SAVE 3
T1 *CONNSER
AT1  C     1
AT2  N     2
AT3  C     3
AT4  N     2
AT5  C     2
AT6  N     1
AT7  N     2
AT8  C     2
AT9  C     2
AT10  S     2
AT11  C     2
AT12  C     3
AT13  N     2
AT14  C     2
AT15  N     2
AT16  C     3
AT17  C     1
BO     1     2 99
BO     2     3 99
BO     3     4 99
BO     3     7 99
BO     4     5 99
BO     5     6 99
BO     7     8 99
BO     8     9 99
BO     9    10 99
BO    10    11 99
BO    11    12 99
BO    12    13 99
BO    12    16 99
BO    13    14 99
BO    14    15 99
BO    15    16 99
BO    16    17 99
END
QUESTION T1
---------+---------+---------+---------+---------+---------+---------+---------+
CABBAI
4-(2-(2-Cyano-3-methyl-3-nitroso-1-guanidino)-ethylthiomethyl)-5-methylimidazoli
      um nitrate
N-Nitroso-cimetidine nitrate
higher-melting polymorph, potential carcinogenic agent
C10 H16 N7 O1 S1 1+,N1 O3 1-
K.Burns,K.Prout,G.J.Durant
J.Chem.Soc.,Perkin Trans.2, , 1239,1983
---------+---------+---------+---------+---------+---------+---------+---------+
CADVIM
N-Cyano-N'-methyl-N''-(2-(((5-methyl-1H-imidazol-4-yl)-methyl)thio)ethyl)-guanid
      ine monohydrochloride monohydrate
Cimetidine monohydrochloride monohydrate
histamine H2-receptor antagonist activity
C10 H17 N6 S1 1+,Cl1 1-,H2 O1
M.Shibata,M.Kagawa,K.Morisaka,T.Ishida,M.Inoue
Acta Crystallogr.,Sect.C (Cr.Str.Comm.), 39, 1255,1983
---------+---------+---------+---------+---------+---------+---------+---------+
CIMETD
N''-Cyano-N-methyl-N'-(2-((5-methyl-1H-imidazol-4-yl)-methylthio)-ethyl)-guanidi
      ne
Cimetidine
monoclinic form A, histamine H2-receptor antagonist activity
C10 H16 N6 S1
E.Hadicke,F.Frickel,A.Franke
Chem.Ber., 111, 3222,1978
---------+---------+---------+---------+---------+---------+---------+---------+
CIMETD01
N-Cyano-N'-methyl-N''-(2-((5-methyl-1H-imidazol-4-yl)methylthio)ethyl)-guanidine

Cimetidine
monoclinic form z, histamine H2-receptor antagonist activity
C10 H16 N6 S1
L.Parkanyi,A.Kalman,B.Hegedus,K.Harsanyi,J.Kreidl
Acta Crystallogr.,Sect.C (Cr.Str.Comm.), 40, 676,1984
---------+---------+---------+---------+---------+---------+---------+---------+
CIMETD02
Cimetidine
N''-Cyano-N'-methyl-N-(2-((5-methyl-1H-imidazol-4-yl)methylthio)ethyl)guanidine
powerful histamine antagonistic activity
C10 H16 N6 S1
S.R.Critchley
Private Communication, , ,1979
---------+---------+---------+---------+---------+---------+---------+---------+
CIMETD03
Cimetidine
N''-Cyano-N'-methyl-N-(2-((5-methyl-1H-imidazol-4-yl)methylthio)ethyl)guanidine
powerful histamine antagonistic activity
C10 H16 N6 S1
R.J.Cernik,A.K.Cheetham,C.K.Prout,D.J.Watkin,A.P.Wilkinson,B.T.M.Willis
J.Appl.Crystallogr., 24, 222,1991
---------+---------+---------+---------+---------+---------+---------+---------+
CIMGUA
2-Cyano-1-methyl-3-(2-((5-methyl-1H-imidazol-4-yl)-methylthio)-ethyl)-guanidine 
      monohydrate
C10 H16 N6 S1,H2 O1
B.Kojic-Prodic,Z.Ruzic-Toros,N.Bresciani-Pahor,L.Randaccio
Acta Crystallogr.,Sect.B, 36, 1223,1980
---------+---------+---------+---------+---------+---------+---------+---------+
CMTCUA
bis(mu!2$-Cimetidine)-copper(ii) diperchlorate monohydrate
antiulcer drug complex
(C20 H32 Cu1 N12 S2 2+)n,2n(Cl1 O4 1-),n(H2 O1)
F.T.Greenaway,L.M.Brown,J.C.Dabrowiak,M.R.Thompson,V.M.Day
J.Am.Chem.Soc., 102, 7782,1980
---------+---------+---------+---------+---------+---------+---------+---------+
CMTCUB
(Methoxyimino-cimetidine-N,N',N'',S)-perchlorato-copper(ii) perchlorate
antiulcer drug complex
C11 H20 Cl1 Cu1 N6 O5 S1 1+,Cl1 O4 1-
F.T.Greenaway,L.M.Brown,J.C.Dabrowiak,M.R.Thompson,V.M.Day
J.Am.Chem.Soc., 102, 7782,1980
---------+---------+---------+---------+---------+---------+---------+---------+
CONYUZ
bis(Cimetidine-N,S)-copper(ii) diperchlorate
C20 H32 Cu1 N12 S2 2+,2(Cl1 O4 1-)
A.Sancho,J.Borras,L.Soto,C.Esteban-Calderon,M.Martinez-Ripoll,S.Garcia-Blanco
Acta Crystallogr.,Sect.A (Fnd.Cryst.), 40, C103,1984
---------+---------+---------+---------+---------+---------+---------+---------+
CONYUZ10
catena(bis(N-Cyano-N'-methyl-N''-(2-((5-methyl-1H-imidazol-4-yl)methylthio)ethyl
      )guanidine-N,N',S)-copper(ii) diperchlorate)
catena(bis(Cimetidine-N,N',S)-copper(ii) diperchlorate)
(C20 H32 Cu1 N12 S2 2+)n,2n(Cl1 O4 1-)
A.Sancho,J.Borras,L.Soto-Tuero,C.Esteban-Calderon,M.Martinez-Ripoll,S.Garcia-Bla
      nco
Polyhedron, 4, 539,1985
---------+---------+---------+---------+---------+---------+---------+---------+
DEFWEQ
bis(N-Cyano-N'-methyl-N''-(2-(((5-methyl-1H-imidazol-4-yl)-methyl)-thio)-ethyl)-
      guanidine)-copper(ii) dinitrate
bis(Cimetidine)-copper(ii) dinitrate
(C20 H32 Cu1 N12 S2 2+)n,2n(N1 O3 1-)
L.Soto,J.Borras,A.Sancho,A.Fuertes,C.Miravitlles
Acta Crystallogr.,Sect.C (Cr.Str.Comm.), 41, 1431,1985
---------+---------+---------+---------+---------+---------+---------+---------+
DOKGAL
bis(Cimetidine)-cobalt(ii) diperchlorate
bis(N-Cyano-N'-methyl-N''-(2-((5-methyl-1H-imidazol-4-yl)-methylthio)ethyl)guani
      dine)-cobalt(ii) diperchlorate
(C20 H32 Co1 N12 S2 2+)n,2(Cl1 O4 1-)
A.Sancho,L.Soto-Tuero,A.Cantarero,M.I.Arriortua,J.M.Amigo
Z.Kristallogr., 173, 155,1985
---------+---------+---------+---------+---------+---------+---------+---------+
DOKGEP
bis(Cimetidine)-nickel(ii) diperchlorate
bis(N-Cyano-N'-methyl-N''-(2-((5-methyl-1H-imidazol-4-yl)-methylthio)ethyl)guani
      dine)-nickel(ii) diperchlorate
(C20 H32 N12 Ni1 S2 2+)n,2(Cl1 O4 1-)
A.Sancho,L.Soto-Tuero,A.Cantarero,M.I.Arriortua,J.M.Amigo
Z.Kristallogr., 173, 155,1985
---------+---------+---------+---------+---------+---------+---------+---------+
GAXVUW
catena(bis(N-Cyano-N'-methyl-N''-(2-((5-methyl-1H-imidazol-4-yl)methylthio)ethyl
      )guanidine-N''',N'''',S)-nickel bis(tetrafluoroborate))
(C20 H32 N12 Ni1 S2 2+)n,2n(B1 F4 1-)
J.M.Amigo,M.M.Reventos,A.Sancho,L.Soto-Tuero,A.Cantarero
Z.Kristallogr., 180, 123,1987
---------+---------+---------+---------+---------+---------+---------+---------+
GEWYUC
catena(bis(mu!2$-Cimetidine-N,N',S)-copper(ii) sulfate nonahydrate)
catena(bis(mu!2$-N-Cyano-N'-methyl-N''-(2-((5--methyl-1H-imidazol-4-yl)methylthi
      o)ethyl)guanidine-N,N',S)-copper(ii) sulfate nonahydrate)
(C20 H32 Cu1 N12 S2 2+)n,n(O4 S1 2-),9n(H2 O1)
L.Soto,J.P.Legros,A.Sancho
Polyhedron, 7, 307,1988
---------+---------+---------+---------+---------+---------+---------+---------+
VIYHOA
(5-Methylcimetidine-S,N,N',N'')-copper(ii) perchlorate hemihydrate
C11 H19 Cu1 N6 O1 S1 1+,Cl1 O4 1-,0.5(H2 O1)
A.M.Bianucci,F.Demartin,M.Manassero,N.Masciocchi,M.L.Ganadu,L.Naldini,A.Panzanel
      li
Inorg.Chim.Acta, 182, 197,1991
---------+---------+---------+---------+---------+---------+---------+---------+
VIYHUG
(5-Methylcimetidine-S,N,N',N'')-copper(ii) iodide hemihydrate
C11 H19 Cu1 N6 O1 S1 1+,I1 1-,0.5(H2 O1)
A.M.Bianucci,F.Demartin,M.Manassero,N.Masciocchi,M.L.Ganadu,L.Naldini,A.Panzanel
      li
Inorg.Chim.Acta, 182, 197,1991

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