Preheat oven to 325 degrees. Line 40 standard muffin cups with cupcake liners and set aside.
In a medium bowl, whisk together flour, baking soda, baking powder, and salt; set aside.
In the bowl of an electric mixer fitted with the paddle attachment, cream together sugar and butter until light and fluffy, 3 to 5 minutes. Add chocolate and beat on medium speed until well combined, 1 to 2 minutes. Add eggs, 1 at a time, mixing well after each addition. Add sour cream and vanilla and mix until well combined, 1 to 2 minutes.
With mixer on low speed, add flour mixture in three parts, alternating with 1 cup water and beginning and ending with flour; beat until just combined, 1 to 3 minutes.
Fill prepared muffin cups three-quarters full with batter. Transfer to oven and bake for 10 minutes. Rotate muffin pans and continue baking until a cake tester inserted into the center of a cupcake comes out clean, about 10 minutes more. Let cool completely before frosting.
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