Preheat the oven to 350°.
In a small bowl, mix together flour, cocoa, baking soda, baking powder, and salt.
In a large bowl, mix together sugar, oil, and eggs until smooth.
Whisk in vanilla.
Alternately whisk in flour mixture and coffee, making three additions of flour mixture and two of coffee, beating until smooth.
Stir in chocolate chips.
Scoop batter into paper liners in muffin tins.
Bake at 350° for 20-25 minutes or until tops of cupcakes spring back when lightly touched.
Let cool in pans on wire rack for 10 minutes.
Remove from pans and let cool completely on rack.
Top cooled cupcakes with frosting.