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2.7.4 2D Chemical Connectivity Tests

In QUEST3D the composition of 2D chemical connectivity tests is accomplished using:

• the BUILD menu - see (a) below - to build the skeleton fragment

• the 2D-CONSTRAIN sub-menu - see (b) below - to apply constraints to the skeleton fragment, eg. the number of attached hydrogen atoms.

Ex. Does the database contain acetyl bromide?

Suppose that the skeleton fragment shown in (a) has been built using the element types and bond types indicated in the menu options. Details of the building of a skeleton are discussed in chapter 6.

• Select 2D-CONSTRAIN

• The BUILD menu is replaced by the 2D-CONSTRAIN sub-menu - (b) above.

  Select a MENU command, or select an ATOM or BOND to display its properties.
  

• 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>

• Move the cursor over the required ATOM and click a BUTTON.

  (Select another command to end HYDROGENS)

• Select atom 1

• The fragment is now as shown in (b) above.

• Select DEFINE-STRUCTURE

• The BUILD menu is restored and after a few seconds the connectivity bit screens scroll through the dialogue area, terminated by:

  Total Number of Screens Set = 26

Selection of DEFINE-STRUCTURE declares that the 2D connectivity test formulation is complete.

At this point the instruction document would contain:

T1  *CONN
NFRAG  1
AT1  C   1  3                    :XY 151 601
AT2  C   3                       :XY 500 601
AT3  O   1                       :XY 849 601
AT4  Br  1                       :XY 500 399
BO  1  2  1
BO  2  3  2
BO  2  4  1
END

It can be seen that a 2D connectivity test starts with Tn *CONN and ends with END. The total set of instructions constitutes a 2D connectivity test packet.

Basic QUEST Procedure

In QUEST the test would be composed by typing the above instruction document with omission of the XY diagram coordinates; also NFRAG 1 is a default instruction and would not normally be typed for QUEST. Details of the atom property records ATn and bond property records BO are given in chapter 6.

2.7.5 3D Geometric Calculations and Tests

Graphics QUEST3D Procedure

Ex. Find all entries in which a nitrogen atom lies in the range 6-8Å from the oxygen atom of a phenol ring.

Suppose that the phenol ring and one N atom have been constructed with the BUILD menu and 2D- CONSTRAIN sub-menu.

• We now select the 3D-CONSTRAIN sub-menu from the BUILD menu.

  The command DEFINE PARAMETER is then used to define the distance from atom 8 to atom 7 and this parameter is named N...O

  This command is displayed in the top-left of the drawing area.

• The command SELECT is then used to specify that the parameter N...O has limiting values 6.0 and 8.0Å.

  This command is then displayed in the top-left of the drawing area.

• Finally DEFINE-STRUCTURE is selected to declare that the test formulation is complete.

  At this point the instruction document would contain:

T1 *CONN
NFRAG   1
AT1 C 2                                            :XY   100   685
AT2 C 2                                            :XY   260   777
AT3 C 2                                            :XY   420   685
AT4 C 2                                            :XY   420   500
AT5 C 3                                            :XY   260   408
AT6 C 2                                            :XY   100   500
AT7 O 1 1                                          :XY   260   223
AT8 N 0                                            :XY   900   223
BO 1 2 5
BO 2 3 5
BO 3 4 5
BO 4 5 5
BO 5 6 5
BO 1 6 5
BO 5 7 1
GEOM
DEFINE N...O 8 7
SELECT N...O 6.0 8.0
C Overlap of crystal fragments permitted
C Search for ALL crystal fragments
NFRAG -99
ENANT NOIN
END

Full details of the specification of 3D constraints are given in chapter 7. It is sufficient to note that the instruction document is composed of:

• the 2D chemical connectivity search packet - lines T1 *CONN to BO 5 7 1
• the 3D crystal constraints - lines GEOM to END

Basic QUEST

There is no equivalent facility in Basic QUEST. Instructions of the type GEOM to ENANT in the above example are invalid in Basic QUEST.

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