Chrome removed the launchpad to launch single-window web apps, but it's easy to create a desktop launcher.

First install chromium:

sudo apt-get install chromium-browser

Now, right-click desktop, add launcher and configure as following:

click on rocket icon to change icon.
Name: WhatsApp
Command: chromium-browser --app=http://web.whatsapp.com

confirm. Add to menu when asked (if desired).