Preheat oven to 325°F and line muffin tin with cupcake liners.
In a medium-sized bowl, whisk together the flour, cocoa powder, baking powder, baking soda, and salt until combined.
In a separate, large bowl, add the water, buttermilk, oil, egg, egg yolk, and vanilla. Whisk together until thoroughly mixed.
Add the sugar to the wet ingredients and whisk to incorporate.
Add the flour mixture to the wet ingredients in three parts, whisking until just combined before each addition. Be careful not to over mix, you only want to mix until no streaks of flour remain. Not over-mixing will allow for the most tender cupcake.
Pour into the lined muffin tin, filling each well a little over halfway full.
Bake for 12-15 minutes, and check with a toothpick for done-ness.
Let cool for at least 30 minutes before attempting to frost.