Volume 2 Chapter 2 2D-Constrain Sub-menu GENERATE-HYDS

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HYDROGENS

Function

HYDROGENS is used to specify the number of terminal hydrogen atoms attached to an atom.

Examples

Ex. 1 Suppose we wish to search for choline derivatives of the type (i) - see below.

Suppose we have built the fragment (ii).

Ex. 2 Suppose we have built fragment (i) - see below.

Suppose we will allow either 1 or 2 terminal H atoms on atom a.

If a search was conducted with fragment (ii) then hits would be registered for (iii) and (iv) but not (v) since it contains 3 terminal H atoms.

Multiple values are linked by `OR' when the search is conducted.

Ex. 3 Suppose we have constructed the fragment:

Suppose we wish to remove the HYDROGENS specification from the N atom:

Ex. 4 Consider the fragment:

This has been built using the PERIODIC TABLE sub-menu to select the H and AA element symbols.

Thus we have specified explicit terminal H atoms for the methyl group.

The more common procedure would have been to assign these H atoms using the HYDROGENS command in the 2D-CONSTRAIN sub-menu. This assignment of implicit terminal H atoms would have resulted in:

You should note that either fragment will produce the same `hits' when a search is conducted.

Tautomerism

Consider the fragments:

(i) and (ii) are keto-enol tautomers

(ii) is fully aromatic and can be represented by (iii).

QUEST and QUEST3D do not recognise the possibility for tautomerism in a search fragment and thus care must be taken in conducting such a search.

When a new entry is input to the database, the tautomer is formulated to correspond to the results of the crystal structure determination; if the published structure is inconclusive with respect to tautomerism then an arbitrary choice is made.

CSD chemical classes with the greatest number of tautomeric problems are classes:

44: Pyrimidines and Purines

47: Nucleosides and Nucleotides

Therefore the greatest care should be taken to consider the tautomeric aspects of a search structure when these classes are involved.

If these fragments correspond to tests T1 and T3 then, to avoid missing relevant hits, the search question should be T1 .OR. T3.

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Volume 2 Chapter 2 2D-Constrain Sub-menu MIN-CONNECTIONS.