Volume 1 Chapter 6 ELDEL in Basic QUEST

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6.2.8 Atom Property Record - Exact Value of mca

Atom property record ATp el mca nh nch E Tn A/C

When E is specified in the atom property record QUEST interprets the value of mca as the exact number of connected atoms, excluding terminal H atoms.

This facility can be useful to restrict the level of substitution at an atom.

Ex. If, in test T1, you specify for atom 1

AT1  TR  6  E

then hits will be registered only for (c).

6.2.9 Atom Property Record - nh Value

Atom property record ATp el mca nh nch E Tn A/C

The value of nh specifies the number of attached terminal H atoms.

The value can be either a single integer, or a set of alternative values separated by commas.

In many searches the value of nh is not specified to allow for various levels of substitution.

Ex. Consider the search fragment (a) below, with its associated search question.

(a)

T1  *CONN
AT1  C  1  1,2
AT2  O  2
AT3  C  3
AT4  C  1
AT5  C  1
AT6  C  1
BO  1  2  C
BO  2  3  C
BO  3  4  C
BO  3  5  A
BO  3  6  A
END
QUES  T1

Atom 1 is allowed to have 1 or 2 attached terminal H atoms.

A search using the test T1 will register hits for (i) and (ii) but not (iii).

Special notes are provided later in this chapter on the subject of implicit and explicit hydrogen atoms.

In specifying the value of nh you should always consider whether the search fragment is capable of tautomerism.

When a new entry, capable of tautomerism, is input to the database it 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.

QUEST does not analyse a search fragment for tautomeric forms and thus if the search fragment is capable of tautomerism then you should consider running separate searches for the individual forms. Alternatively you can run a single search with the forms expressed as separate connectivity tests linked by the .OR. logical operator.

6.2.10 Atom Property Record - Total Coordination Number

Atom property record ATp el mca nh nch E Tn A/C

The total coordination number, Tn, is the total number of attached atoms, including terminal H atoms.

Tn is a very powerful feature which can be used to discriminate between different hybridisation states and it has, of course, applications for metal complex structures.

Ex.1 Consider the search fragment (a) below, with its associated search question.

(a)

T1  *CONN
AT1  C  1  1,2
AT2  O  2
AT3  C  3
AT4  C  1
AT5  C  1
AT6  C  1
BO  1  2  C
BO  2  3  C
BO  3  4  C
BO  3  5  A
BO  3  6  A
END
QUES  T1

Suppose we were to replace the atom property record for atom 1 by: AT1 C T4

This implies that carbon atom 1 should have sp-3 hybridisation.

A search using this redefined test T1 would register a hit for (ii) but not for (i) or (iii).

Ex.2 Consider the search fragment (b) below, with its associated search question.

(b)

T2  *CONN
AT1  IR  T6
END
QUES  T2

A search using test T2 would register hits for (iv) and (v).

Suppose we were to replace the atom property record for atom 1 by: AT1 IR 6 E

A search using this redefined test T2 would register a hit for (iv) but not for (v).

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Volume 1 Chapter 6 Atom Property Record nch Value.