In a medium heatproof bowl, combine the chocolate, cocoa powder, and espresso powder. Pour hot water over mixture. Cover and let stand for 5 minutes. Whisk mixture gently until smooth, then set aside to cool.
Meanwhile, preheat oven to 350°F. Line a standard 12-cup muffin tin with paper liners.
In a small bowl, whisk together the flour, sugars, salt, and baking soda.
Whisk sour cream, oil, eggs, egg yolk, vinegar, and vanilla into the cooled chocolate mixture until smooth, scraping down the sides and bottom of the bowl as you mix. Stir in the flour mixture until smooth, being careful not to overmix.
Using a spring-loaded scoop, divide the batter evenly among prepared muffin cups until ¾ full. Bake until cupcakes are set and firm to the touch, about 17 to 18 minutes.
Let cupcakes cool in pan on a wire rack for 10 minutes before removing from pan to cool completely, about 1 hour. Cupcakes can be stored in an airtight container at room temperature for up to 1 day.