Back to Table of Contents
We refer to this handling as the implicit treatment of hydrogen atoms.
If you so wish, connectivity tests can be expressed in terms of explicit hydrogen atoms but this is not normally done since it involves the typing of more lines of atom property records.
Consider the search fragment: C-NH2
This can be formulated in the three ways (a)-(c) shown below:
(a) T1 *CONN (b) T2 *CONN (c) T3 *CONN AT1 C 1 AT1 C 1 AT1 C 1 AT2 N 1 2 E AT2 N 3 0 E AT2 N 2 1 E BO 1 2 AT3 H 1 AT3 H 1 END AT4 H 1 BO 1 2 QUES T1 BO 1 2 BO 2 3 BO 2 3 END BO 2 4 QUES T3 END QUES T2
However, you should bear in mind that if the search fragment contains several characteristic features, such as unusual elements and ring systems, then you might choose to ignore bond types by setting them to bond type 99, ie. any bond type. The disadvantages of this approach are that the search may run much more slowly and the number of unwanted hits may be unacceptably high.
A few of the more important conventions are listed below:
However, there are some situations where bt=5 is used in other ring systems. Equally there are cases where the author strongly suggests localisation of double bonds and these are coded as alternating bt=1 and bt=2.
If in doubt you should use a variable bond type setting: bt=1,2,5
For such structures you should use a variable bond type setting: bt=1,2,7
For isolated ring ligands such as cyclopentadienyl and benzene the connectivity record in the database contains only one pi-bond from the metal to one atom of the ring.
For other ligands the individual pi-bonds are assigned explicitly, as indicated in the publication.
If the search fragment involves an unsubstituted isolated ring ligand then there is no difficulty but if the ring is substituted you should use the variable point of attachment feature. An example is shown below to illustrate the procedure.
T1 *CONN C FURTHER SUBSTITUTION IS ALLOWED AT ATOMS 3-6 AT1 FE 1 AT2 C 3 AT3 C 2 AT4 C 2 AT5 C 2 AT6 C 2 AT7 C 1 3 E BO 1 2, 3, 4, 5, 6 9 BO 2 3 5 BO 3 4 5 BO 4 5 5 BO 5 6 5 BO 6 2 5 BO 2 7 END QUES T1
Suppose the search fragment involves an iron atom pi-bonded to methylcyclopentadienyl.
For any target structure in the database you do not know to which atom of the ring the iron atom is pi-bonded. Therefore, to be sure of hitting all relevant structures you must code a variable point of attachment of the iron atom.
In the example Fe1 is shown to be pi-bonded to atoms 2 or 3 or 4 or 5 or 6.
In fact, you could make use of the topological symmetry of the substituted ring and simply indicate bonding to 2 or 3 or 4 , since atoms 3 and 6 are equivalent, likewise atoms 4 and 5.
Volume 1 Chapter 6 2D Searching in Graphics QUEST3D.