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HYDROGENS

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).

• Select HYDROGENS

• Type EXACT number of terminal HYDROGENS.
  You may use multiple values, separated by SPACE or COMMA
  (Press <RETURN> to mean "Unspecified")

• Type 3 <R>

  3 appears in the HYDROGENS box.

• Move the cursor over the required ATOM and click a BUTTON.
  (Select another command to end HYDROGENS)

• Select atom p, then atom q, then atom r

  The fragment is now as in (iii).

  

• Select HYDROGENS

  3 vanishes form the HYDROGENS box.

• Type EXACT number of terminal HYDROGENS.
  You may use multiple values, separated by SPACE or COMMA
  (Press <RETURN> to mean "Unspecified")

• Type 2 <R>

  2 appears in the HYDROGENS box.

• Move the cursor over the required ATOM and click a BUTTON.
  (Select another command to end HYDROGENS)

• Select atom s, then atom t

  The fragment is now as in (iv).

  

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

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

• Select HYDROGENS

• Type EXACT number of terminal HYDROGENS.
  You may use multiple values, separated by SPACE or COMMA
  (Press <RETURN> to mean "Unspecified")

• Type 1,2 <R>

  1,2 appears in the HYDROGENS box.

• Move the cursor over the required ATOM and click a BUTTON.
  (Select another command to end HYDROGENS)

• Select atom a

  The fragment is now as in (ii).

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:

• Select HYDROGENS

• Type EXACT number of terminal HYDROGENS.
  You may use multiple values, separated by SPACE or COMMA
  (Press <RETURN> to mean "Unspecified")

• Press <R>

  Un appears in the HYDROGENS box.

• Move the cursor over the required ATOM and click a BUTTON.
  (Select another command to end HYDROGENS)

• Select N atom

  The fragment is now:

  

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.