Adjust oven rack to the middle position and preheat oven to 325°F. Line a 12-cup muffin tin with cupcake liners and set aside.
In a small bowl, combine flour, baking soda, and salt. Set aside.
In a large bowl, whisk cocoa powder, chocolate chips, espresso powder, and boiling water until smooth and combined (the chocolate chips should be completely melted). Add sour cream, oil, eggs, sugar, extracts, and orange zest and whisk until well combined. Add the flour mixture and whisk until combined. If necessary, use a rubber spatula to scrape the sides and bottom of the bowl.
Fill the prepared muffin cups about two-thirds to three-quarters full. Depending on the size of your muffin cups you might have a few tablespoons of batter leftover.
Bake for 18-22 minutes, until a toothpick inserted into the center comes out with a few crumbs attached, but no raw batter. Be careful not to overbake. Place the pan on a wire rack to cool for 10 minutes, then remove the cupcakes from the pan and place them directly on the rack to cool completely. Meanwhile, proceed with the frosting.