Preheat the oven to 350 degrees F and line one 12-cup standard muffin tin with paper cupcake liners.
Put the butter, cocoa powder and unsweetened chocolate in a large bowl. Pour over the boiling water and let stand 5 minutes. Whisk until smooth, and then whisk in the sugar, vanilla and eggs. Whisk in the flour, baking powder, salt and baking soda until just combined. Stir in the walnuts or chocolate chips if using. Divide the batter among the prepared liners so they are about three-quarters full.
Bake until a toothpick inserted into the center comes out with moist crumbs, 22 to 24 minutes. Cool in the tins 5 minutes, then remove and cool completely on a wire rack.
For the chocolate glaze:
Put the semisweet chocolate in a medium bowl. Heat the cream in a small saucepan over medium heat until it just simmers. Pour the cream over the chocolate and let sit for 1 minute, then gently stir until smooth and glossy. Cool the glaze slightly until thickened but not hard. Spread 1 tablespoon of glaze on top of each cupcake or dip the tops of the cupcakes into the glaze.
When measuring flour, we spoon it into a dry measuring cup and level off the excess. (Scooping directly from the bag compacts the flour, resulting in dry baked goods.)
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