Heat oven to 325°. Butter and flour an 8 x 8-inch baking pan. Combine flour, cocoa, baking powder, cinnamon, chipotle powder and salt in a medium bowl; set aside.
In a medium saucepan, bring 1 inch of water to a simmer. Add butter, unsweetened chocolate and semisweet chocolate to a metal bowl large enough to sit on top of the saucepan. Melt ingredients, about 4 minutes. Remove from heat and stir until smooth.
In the bowl of a stand mixer fitted with a whisk attachment, combine eggs, sugar and vanilla. Whisk on high speed until slightly thickened, 1 to 2 minutes. Pour in the melted chocolate mixture and whisk on medium for 30 seconds. Add the flour mixture and whisk on low for 30 seconds. Add sour cream and whisk on medium for 30 seconds. Stir in chocolate chunks by hand.
Bake at 325° for 35 minutes, or until a toothpick inserted in the center comes out clean. Cool on wire rack 10 minutes.