Volume 1 Chapter 6 Implicit and Explicit Hydrogen Atoms

In all the examples illustrated earlier in this chapter each hydrogen atom has been terminal and its number has been specified as a property, nh, of the atom to which it is attached.

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

(a): This involves the normal implicit formulation with the N atom having nh=2.
(b): This involves two explicit H atoms numbered as atoms 3 and 4. Note that the N atom now has nh=0 and each H atom has mca=1.
(c): This involves one implicit H atom and one explicit H atom, numbered 3. In this case the N atom has mca=2 and nh=1; H3 has mca=1.

However, you must note that there are 3 situations in which explicit hydrogen atoms are used in the database:

bridging H atoms
- An example would be B-H-B in carborane structures
deuterium atoms
- If the structure is deuterated then the D atoms are specified explicitly in the connection table.
structures where a residue contains only C-H bonds.
- An example would be methyl potassium CH3- K+
Note that if you construct a search test for the CH3 fragment then the search will be extremely slow unless you can combine the test with other tests to improve the screenout. For example, you could use the fact that such simple carbanions are assigned to basic chemical class 12.

6.2.23 Bond Type Conventions in the Database

In constructing a connectivity test it is useful to be aware of the principal conventions used in assigning bond types to structures.

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:

Bond type 5 (aromatic) is used for equivalent/aromatic bonds in 6-membered rings and in the cyclopentadienyl ring.
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
A similar problem of localised vs. delocalised double bonds occurs with compounds such as acetylacetonates, thiocarbamates, xanthates, thiathiophthenes, etc. Our policy is to assign bond types according to the author's description of the structure.
For such structures you should use a variable bond type setting: bt=1,2,7
Terminal carbonyl groups have bt=3, whereas bridging carbonyl groups have bt=2.
In some publications it is rather difficult to decide whether a bond exists between a metal atom and a potential ligand atom, especially when the interatomic distance is unusually large. This bond : no-bond problem should be borne in mind if you are conducting a search for transition elements with a specified coordination number. Similar problems arise with complexes of crown ethers, cryptates, etc. and the metals of groups 1A and 2A.
There is a special problem associated with pi-bonding, bt=9.
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.

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Volume 1 Chapter 6 2D Searching in Graphics QUEST3D .

6.2.22 Implicit And Explicit Hydrogen Atoms

6.2.23 Bond Type Conventions in the Database