Tutorial 3.1 Building Perfluoroanthracene

Step 1
Start the builder by typing pqsmol at the command prompt.

First we are going to construct the parent compound, perfluoroanthracene. This comprises three fused aromatic rings, and we are going to build this from two existing fragments: benzene in the MONOCYCLIC fragment library, and naphthalene in the BICYCLIC fragment library.

Step 2
Insert the naphthalene fragment

In the Segment window select the Fragments tab, then select BICYCLIC. Scroll down to select naphthalene. Insert the Naphthalene fragment into the build area, either by using the Default tool and right-clicking or by using the Add/Attach/Connect tool Image insert. At this point the Build window is shown in Figure [*].

Image t3-1
Build window - inserting the naphthalene fragment

Step 3
Insert the benzene fragment

Now select the MONOCYCLIC fragment library and select benzene. Move the mouse pointer into the Build window and insert the fragment in the empty space to the right of the naphthalene fragment. This should add the benzene fragment into the Build window as shown in Figure [*].


Image 1-2
Build window - inserting the benzene fragment

As shown, the benzene fragment is oriented differently from the naphthalene fragment. It can be reoriented into the build plane by selecting the Reorient Selection tool Image reorient and clicking on any atom in the benzene fragment; the atom will be highlighted with a green translucent sphere and the fragment can be reoriented by dragging the mouse vertically. The result is shown in Figure [*].

Image 1-3
Build window - reorienting the benzene fragment

Step 4
Fuse the naphthalene and benzene fragments

Select the Bond Fuse tool Image bondfuse. Click on the (approximately) vertical ring bond in the naphthalene fragment closest to the benzene. Click on the corresponding bond in the benzene fragment. The two rings will be fused at the selected bonds. When the segments are fused, the newly fused bond is automatically defined as a rotation bond and designed with a white torus, Figure [*].

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Build window - fusing the naphthalene and benzene fragments, attachment

Drag the mouse to rotate about the rotation bond, or select the dihedral angle (180{\circ}) from the rotation preset window that automatically appears. The final result should be as shown in Figure [*].


Image 1-5
Build window - fusing the naphthalene and benzene fragments, rotation

Double click inside the build area to clear the selection and set the angle.

Step 5
Add the fluorine atoms

Select Building Blocks tab in the Segment window and select fluorine from the periodic table. In the default Sybyl 5.2 force field there is only one fluorine building block which will be shown in the Segment buffer. Select the Add/Attach/Connect tool Image insert and replace every ring hydrogen atom by fluorine. You have now built perfluoroanthracene, Figure [*].

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Build Window - hydrogen replaced with fluorine

The structure can be optimized by clicking on the Optimize button Image optimize and the symmetry found by clicking on the Check Symmetry button . The resulting point group should be d2h, Figure [*].

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Symmetry dialog

The entire procedure up to this point could have been considerably simplified, as the POLYCYCLIC fragment library already contains an Anthracene fragment, which could have been selected directly instead of fusing the naphthalene and benzene rings. But where's the fun in that?