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TitleIsoStar User Guide and Tutorials
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IsoStar User Guide and Tutorials

2016 CSDS Release

Copyright © 2015 Cambridge Crystallographic Data Centre

Registered Charity No 800579

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ii IsoStar User Guide and Tutorials

Conditions of Use

The Cambridge Structural Database System (CSD System) comprising all or some of the

ConQuest, Quest, PreQuest, deCIFer, Mercury, (Mercury CSD and CSD-Materials [formerly
known as the Solid Form or Materials module of Mercury], Mercury DASH), Mogul, IsoStar,
DASH, SuperStar, web accessible CSD tools and services, WebCSD, CSD Java sketcher, CSD
data file, CSD-UNITY, CSD-MDL, CSD-SDfile, CSD data updates, sub files derived from the
foregoing data files, documentation and command procedures, test versions of any existing
or new program, code, tool, data files, sub-files, documentation or command procedures
which may be available from time to time (each individually a Component) is a database and
copyright work belonging to the Cambridge Crystallographic Data Centre (CCDC) and its
licensors and all rights are protected. Use of the CSD System is permitted solely in
accordance with a valid Licence of Access Agreement or Products Licence and Support
Agreement and all Components included are proprietary. When a Component is supplied
independently of the CSD System its use is subject to the conditions of the separate licence.
All persons accessing the CSD System or its Components should make themselves aware of
the conditions contained in the Licence of Access Agreement or Products Licence and
Support Agreement or the relevant licence.

In particular:

The CSD System and its Components are licensed subject to a time limit for use by a
specified organisation at a specified location.

The CSD System and its Components are to be treated as confidential and may NOT
be disclosed or re-distributed in any form, in whole or in part, to any third party.

Software or data derived from or developed using the CSD System may not be
distributed without prior written approval of the CCDC. Such prior approval is also
needed for joint projects between academic and for-profit organisations involving
use of the CSD System.

The CSD System and its Components may be used for scientific research, including
the design of novel compounds. Results may be published in the scientific literature,
but each such publication must include an appropriate citation as indicated in the
Schedule to the Licence of Access Agreement or Products Licence and Support
Agreement and on the CCDC website.

No representations, warranties, or liabilities are expressed or implied in the supply
of the CSD System or its Components by CCDC, its servants or agents, except where
such exclusion or limitation is prohibited, void or unenforceable under governing

Licences may be obtained from:

Cambridge Crystallographic Data Centre
12 Union Road
Cambridge CB2 1EZ, United Kingdom

Telephone: +44-1223-336408
Email: [email protected]

(UNITY is a product of Certara and MDL is a registered trademark of BIOVIA)

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IsoStar User Guide and Tutorials 47

7.6 Aromatic I ... any C,N,O,S or H
 A particularly good way of spotting novel interactions is to look at scatterplots

involving the contact group any C,N,O,S or H.
 For example, the CSD-based plot for any C,N,O,S or H around aromatic iodine shows

several C-I..O contacts along the extension of the C-I bond (Lommerse et al, J. Am.
Chem. Soc., 118, 3108, 1996). Some of these are extremely short (contacts less than
the sum of van der Waals radii are shown below).

 Short, highly directional sulfur...oxygen and sulfur...nitrogen contacts (Burling &
Goldstein, J. Am. Chem. Soc., 114, 2313, 1992) are found in the plot of any C,N,O,S or
H around sulfur heterocycles (contacts shorter than the sum of van der Waals radii -
0.3 Å are shown below).

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48 IsoStar User Guide and Tutorials

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IsoStar User Guide and Tutorials 99

 Hit OK.
 Now hit the IsoGen top-level menu button Run again. A new scatterplot will be

calculated. Don’t worry if you get some warning messages from the program - if
necessary, just hit OK to remove them. When the pop-up window appears asking if
you want to view the scatterplot, select Yes. You should now see the various
orientations of the methyl group shown explicitly, something like this:

 Close the IsoStar graphical interface and hit OK in the IsoGen text window.

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100 IsoStar User Guide and Tutorials

Omitting Atoms
 Another thing we can do is omit conformationally variable atoms altogether. First,

we need to undo our previous Flexible atoms definition. Select Expert from the
IsoGen top-level menu and Flexible atoms... from the sub-menu. Delete the
numbers from the white box in the resulting pop-up window, and hit OK.

 Now select the IsoGen option Expert and then Omit atoms.... The search fragments
are again displayed in a pop-up window. Pick the methyl-group H atoms and hit OK.

 Hit Run in the IsoGen window to re-compute the scatterplot. This time, as you will
see, the hydrogens of the methyl group are not displayed at all.

 Finally, remove the windows that remain from the tutorial. The main IsoGen window
can be removed by hitting File and then Exit IsoGen.

This finishes the tutorial, which has demonstrated how to produce scatterplots from the CSD
by performing nonbonded searching in ConQuest and then post-processing the output with
IsoGen. Scatterplots produced in this way may be made accessible from the IsoStar web
page by putting them in the Custom Plots area.

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