Stones are one of my more prominent areas of study. Every stone and gem and natural material has its own metaphysical properties that can be worked with, as well as the capability to hold energy that you send into it.
Now, say you want to charge rose quartz with a harmful energy, its natural inclination is to heal it. You will want to find stones with properties that coincide with your goal. You will have a hard time finding stones whose properties are on the negative side: I think it is just lack of material on the subject; in my experience, stones tend to be very 'neutral', and working with their positive properties is what makes them seem like their only purpose is 'good'.
Stones like obsidian and hematite can enhance negativity. Whereas 'Apache Tear', a type of obsidian, is much more gentle in its healing effects.
I highly recommend "The Crystal Bible" by Judy Hall for identification of crystals and basic properties, and "Love is in the Earth; A Kaleidoscope of Crystals" by Melody for a much larger list of crystals* and more comprehensive examination of the properties.
If there is anything you'd like me to look up, please ask!
* The book also contains materials like petrified wood, amber, fossils, abalone, metals, etc which aren't really 'crystals' but I suppose they are 'gems' in a way :).