Preheat the oven to 350°F. Line 12 standard cupcake wells with liners. Set aside.
In a large bowl, whisk together the flour, sugar, cocoa, baking soda, and salt. Add the vanilla, vinegar, melted butter, and warm water; stir until just combined.
1 1/2 cups all-purpose flour, 1 cup granulated sugar, 3 tablespoons unsweetened cocoa powder, 1 teaspoon baking soda, 1/2 teaspoon fine sea salt, 1 teaspoon vanilla extract, 1 tablespoon white vinegar, 6 tablespoons unsalted butter, 1 cup warm water
Measure about 1/4 cup of batter into each cupcake liner. Bake for 18-20 minutes, or until a toothpick inserted into the center of a cupcake comes out clean.
Allow cupcakes to cool in the pan for about 5 minutes before removing to a wire rack to cool completely before frosting.
Notes
Store unfrosted cupcakes in an airtight container at room temperature for 3-4 days or freeze for up to a month.
The butter can be substituted with dairy-free butter/margarine or shortening for a dairy-free version.
Make this batter into a cake by baking in an 8-inch cake pan at 350°F for 30-35 minutes.