8.2 Ring Fusion Tutorial

The following tutorial illustrates several examples of fusions:

• Fuse Two Planar Bonds
• Fuse Two Rings to Build a Spiro System
• Fuse Two Non Planar Bonds
• Fuse A Planar Bond With A Non Planar Bond

8.2.1 Set Up

1. Clear the SYBYL screen of all molecules and background images.

   Edit > Clear All

2. Set the Screen mode to quartered.

   Click the icon and set the Screen mode to Quartered (press Close).

8.2.2 Fuse Two Planar Bonds

The fusion of two planar systems requires only two pair of atoms. In this example, furan (M1) is fused to pyridine (M2) and the resulting model appears in M2.

1. Read in the two fragments, color them by atom type, and label both structures.

   File > Get Fragment

   Select FURAN (press OK).

   File > Get Fragment

   Select PYRIDINE (press OK).

   Select M2 (press OK).

   View > Display Style > Label > Atom Id

   Highlight M1:furan, click All (press OK).

   View > Display Style > Label > Atom Id

   Select M2:pyridine, click All (press OK).

2. Fuse the two structures.

   Edit > Modify > Fuse Rings

   Click atom 6 in pyridine (M2), and then atom 2 in furan (M1) to form the first pair.

   Click atom 5 in pyridine (M2), and then atom 3 in furan (M1) to form another pair.

   In the Select Atom dialog, press End.

Furan (M1) is fused to pyridine (M2); the resulting model appears in M2.

8.2.3 Fuse Two Rings to Build a Spiro System

You can specify a spiro fusion by first selecting the two atoms that become the spiro center. The second pair involves a ring atom in one molecule and a hydrogen in the other.

1. Read in the two molecules.

   File > Get Fragment

   Select 4H-PYRAN (press OK).

   Select M1 (press OK).

   File > Get Fragment

   Select PIPERIDINE (press OK).

   Select M2 (press OK).

   View > Display Style > Label > Atom Id

   Highlight M1:4H-pyran, click All (press OK).

   View > Display Style > Label > Atom Id

   Select M2:piperidine, click All (press OK).

2. Fuse the two rings.

   Edit > Modify > Fuse Rings

   Click atom 4 in piperidine (M2), and then atom 4 in 4H-pyran (M1) to form the first pair.

   Click atom 12 in piperidine (M2), and then atom 5 in 4H-pyran (M1) to form another pair.

   In the Select Atom dialog, press End.

The two rings are fused with a spiro center; the resulting model appears in M2.

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