Use Basic Chemical Intelligence

    Using basic chemical intelligence in Marvin Pro is as easy as drawing the structures. This example demonstrates how to determine the absolute configuration of stereocenters with the built-in stereo calculation service. It also shows how the aromatization service can be used to easily switch between the two possible representations of aromatic rings.

    1. To use the aromatization/dearomatization function, we need to have a structure on the canvas. For this reason, import or draw a phenylalanine molecule.
    2. Once the structure is on the canvas, you can alternate between the aromatic form and the Kekulé form by clicking the Aromatize/Dearomatize button.

      {info} Aromatization and dearomatization affect the selected structure or structures. If nothing is selected, the aromatize/dearomatize function affects the whole canvas.

      Basic Chemical Intelligence Step 2

    3. To turn on the stereo calculation, hit the Show Stereo button. A blue highlight indicates that the automatic stereo calculation is active.

      Basic Chemical Intelligence Step 3

    4. You can move the stereo labels. To do this, simply drag them.

      {info} Marvin Pro remembers the position of the stereo labels, so when you turn the stereo calculation off, then turn it on again, the labels will be rendered in the same position as before.

      Basic Chemical Intelligence Step 4

    5. Contrary to aromatization/dearomatization, the stereo function does not require a structure. You can toggle it any time and it will calculate the stereo of any newly added structure. Also, the absolute configuration of the structure is recalculated continuously, so the stereo label will be updated as soon as you edit your structure.

      Basic Chemical Intelligence Step 5