For the cupcakes:
½ cup plus 1 tablespoon Dutch-process cocoa powder
½ cup plus 1 tablespoon hot water
2¼ cups all-purpose flour
¾ tsp. baking soda
¾ tsp. baking powder
½ tsp. salt
2 sticks plus 1 tablespoon unsalted butter, at room temperature
1 2/3 cups sugar
3 large eggs, at room temperature
1 tbsp. vanilla extract
¾ cup sour cream
For the caramel and filling:
½ cup sugar
½ cups heavy cream, warmed
1 vanilla bean, split lengthwise (optional)
¼ tsp. coarse salt
½ tsp. vanilla extract
½ cup chopped pecans
For the frosting:
12 oz. cream cheese, cold
12 tbsp. (6 oz.) unsalted butter, at room temperature
6 tbsp. caramel sauce (recipe above)
2¼ cups confectioners’ sugar, sifted
Pinch of coarse salt
Preheat the oven to 350˚ F. Line cupcake pans with paper liners. In a small bowl, combine the cocoa powder and hot water and whisk until smooth. In another medium bowl combine the flour, baking soda, baking powder, and salt, and whisk to blend.
Combine the butter and sugar in a medium saucepan set over medium heat. Cook, stirring occasionally, until the mixture is smooth and the butter is completely melted. Transfer the mixture to the bowl of an electric mixer and beat on medium-low speed until the mixture is cool, about 4-5 minutes. Add the eggs one at a time, mixing well after each addition and scraping down the sides of the bowl as needed. Blend in the vanilla and then the cocoa mixture until smooth. With the mixer on low speed, add the flour mixture in three additions alternating with the sour cream, beginning and ending with the dry ingredients and mixing each addition just until incorporated.
Divide the batter evenly between the prepared liners. Bake until a toothpick inserted in the center comes out clean, about 18-20 minutes, rotating the pans halfway through baking. Let cool in the pan about 5-10 minutes, then transfer to a wire rack to cool completely.
To make the caramel, spread the sugar in an even layer over the bottom of a large, heavy-bottomed saucepan. Place over medium-low heat, watching carefully. When the sugar begins to liquefy around the edges, use a heatproof spatula to gently stir it towards the center. Continue stirring very gently until all the sugar is melted, taking care not to over stir. Measure out the heavy cream in a liquid measuring cup and scrape the seeds from the vanilla bean into the cream. Set aside. Once the caramel reaches a deep amber color, immediately remove the sauce pan from the heat. (To test the color, spoon a drop onto a white plate or bowl.) Carefully pour half of the heavy cream into the saucepan in a steady stream down the edge of the pan, whisking constantly. The mixture will steam and bubble violently. Stir until the cream is well incorporated, then whisk in the remaining cream. Stir in the salt and the vanilla. If any sugar has seized or hardened, place the saucepan over low heat and whisk until smooth. Transfer to a bowl and let cool to room temperature.
To make the frosting, combine the cream cheese, butter, and caramel sauce in the bowl of an electric mixer. Beat on medium-high speed until smooth and creamy, about 2 minutes. Mix in the confectioners’ sugar and salt at medium speed until light and fluffy, about 2 minutes more. Transfer the frosting to a pastry bag with a large round tip (I used Ateco #809). Pipe a swirl of frosting over the top of each cupcake. Use the tip of a small offset spatula or a small spoon to scoop an indentation out of the center of the frosting.
In a small bowl, mix together of the caramel sauce and the chopped pecans. Fill the indentations in the frosting with a small spoonful of the caramel-pecan mixture. Drizzle the cupcakes with additional caramel sauce, chocolate sauce, and sprinkle with additional chopped pecans, if desired.