Volume 1 Chapter 7 Using van der Waals Radii for Distance Testing

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7.14.4 Searching with Functional Groups

All of the contacts encountered up to now have been between single atoms. Sometimes we are interested in how a substructural fragment interacts with another as a whole. The non-bonded search mechanism allows groups of atoms to be defined for use with the CONTACT command. The command is called GROUP.

Ex.8 Suppose we wish to find intermolecular contacts between the carbon or hydrogen atoms of a phenyl group and the oxygen atom of a ketone. In this example we will use the standard van der Waals radii so that hits will be registered for C...O < 4.22Å and H...O < 3.72Å.

The resultant command in the instruction document is: An example of a hit registered by this search is shown below.

H8 is linked by a dotted blue line to O1%.

If you use MEASURE DIST the contact distance is displayed as 2.598Å.

Obviously, the GROUP command must precede the CONTACT in which it will be used since the GROUP label is given in the CONTACT command to identify a set of atoms. The atoms contained in a GROUP must all be from the same substructural fragment. However, an atom may belong to more than one group. It should also be noted that GROUPs can not be used for other geometrical calculations, they relate only to the non-bonded search process (see Volume 2 for SETUP of centroids and other geometric objects).

The inclusion of a GROUP in the CONTACT command generates a question not seen in previous examples. The question prompts the user to indicate how the atoms of the GROUP are to be used in the non-bonded search. One choice is to use the atoms to define a centroid which will be used for the distance test. Obviously, a distance range must be supplied to CONTACT when centroids are used since no van der Waals radii are available for centroids. Alternatively, each atom can be used in turn, atom by atom, for the distance testing. In atom by atom testing, the use of van der Waals distance testing can be very powerful. The table below illustrates the various search options.

Table : Search Options for GROUPs

Consider the interaction between an aromatic ring and the hydrogen atoms of an amino group. The four sets of contacts are illustrated below:

(i) A : A

(ii) C : A

(iii) A : C

(iv) C : C

When the search mechanism locates an intramolecular contact the shortest bond path range test must be applied. If a GROUP is used in the CONTACT command the test is applied to only one atom - the atom that is the shortest bond path from the other search set in the CONTACT. Therefore, only the shortest path between the two sets of the CONTACT is used for the range test.

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Volume 1 Chapter 7 Searches Involving Multiple Contacts.