I want to activate/deactivate synapse with Super key shortcut in Ubuntu 16.04, I tried old solutions in this site but I still can't change the shortcut.
There is no "simple" solution. To assign an action to just pressing the Super key requires a specific tool,
ksuperkey lets you assign any action to pressing and releasing the Super key alone (and other keys if you wish). It will not interfere with uses of the Super key as a modifier for other keys.
ksuperkey is on Github. It is not available in the Ubuntu repositories. Probably, as I did, you will need to compile the utility yourself according to the instructions on the Github page. Do not be afraid: it is an easy compile.
Edit 2019-06-05: A software repository for ksuperkey is available for easier installation: https://launchpad.net/~mehanik/+archive/ubuntu/ksuperkey /Edit
Once loaded, the tool intercepts pressing and releasing Super and remaps that by default to Alt+F1, in many desktops a hotkey for the menuing system. Using command line options, that mapping can be changed.
Thus, create a script that does what you want, in this case toggling synapse. Assign it the hotkey Alt+F1. ksuperkey, which you preferably have autostarted when you log in, will call this hotkey when you press and release kbd>Super.
If you want to preserve the current binding of Alt+F1, then assign another shortcut of your choice to your script. In that case, you will need to autostart
ksuperkey with appropriate command line options to remap to the hotkey you have chosen. Help on the command line options is available on the Github page.