Volume 2 Chapter 1 Build Menu BOND TYPES

Function

These options are used to specify the type of a bond between two atoms.

Remarks

The Current Bond Type is the bond type assigned to newly generated bonds.

It is always highlighted with a box in the bond type area of the BUILD menu.

To change the Current Bond Type simply use the cursor to select the new bond type.

Note that, in MOVE mode, if you select a bond whose type is different from the Current Bond Type then the bond selected is assigned the Current Bond Type.

On entry to the BUILD menu the current bond type is single. This is indicated by the box around SING - see a below.

The various menu options for bond type are:

SING single

DOUB double

TRIP triple

QUAD quadruple

AROM aromatic

POLY polymeric

DELOC delocalised double

PI pi

ANY any

These correspond, in QUEST, to bt = 1, 2, 3, 4, 5, 6, 7, 9, 99.

To change the bond type from the default SING to DOUB

Select DOUB
The red box around SING vanishes and a red box appears around DOUB.

There are two other menu options relating to the construction of bonds:

V. B. T. variable bond type
V. P. A. variable point of attachment.

These are described in the following pages.

V. B. T.

The menu option V. B. T. is used to assign a variable bond type to a bond.

Suppose we wish to search for transition metal carboxylates in which the transition metal is bonded to both oxygen atoms of the carboxylate group.

In the database there may be a mixture of connectivity representations for such structures - see (i) below:

(a) involving localised double and single bonds
(b) involving delocalised double bonds.

To avoid missing any relevant hits we might proceed as follows:

Build the fragment (ii). Ensure that you are in MOVE mode before you continue.

Select V. B. T.

Please use cursor to select the allowed bond types.
Re-select "V. B. T." to complete the definition.
Select CANCEL if you change your mind.

Select SING
Select DOUB
Select DELOC
Select V. B. T.
Select bond x
Bond x is re-drawn as in (iii).
Select bond y
Bond y is re-drawn as in (iv).

Other metal complex systems also involve non-standardised connectivity representations in the database and it is advisable to use variable bond types when searching for them. Important examples are:

(v) with: SS = S, O, N;; RR = S, Se, O;; MM = TR, LN, AN
(vi) with: TT = S, O, N;; MM = TR, LN, AN

V. P. A.

The menu option V. P. A. is used to specify a variable point of attachment.

Suppose we wish to search for o-bromochlorobenzenes and m-bromochlorobenzenes - see (i) below.

We might proceed as follows:

Build the fragment (ii).

Select V. P. A.

Please select the fixed atom of this bond.

Select the Br atom

Please select a possible atom to be bonded to the first
(Select your first atom or V. P. A. to end this operation,
or select "CANCEL" to cancel this bond.)

Select atom a
A bond now links Br to atom a - see (iii). Both atoms are marked by a red cross.

Please select a possible atom to be bonded to the first
(Select your first atom or V. P. A. to end this operation,
or select "CANCEL" to cancel this bond.)

Select atom b
A bond now links Br to atom b - see (iv). Both atoms are marked by a red cross.

Please select a possible atom to be bonded to the first
(Select your first atom or V. P. A. to end this operation,
or select "CANCEL" to cancel this bond.)

Select V. P. A.

The above dialogue assumes that when V.P.A. is first selected, the current program state is MOVE. If, on the other hand, the current program state is DRAW then the active atom will be the fixed atom.

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