Melt the butter in a large pot over medium heat. Add the onion, bell pepper, celery, and 1/2 t salt and cook until vegetables are softened, 6 to 7 minutes, stirring often. Add the garlic, chipotle chile, smoked paprika, thyme, bay leaves, cayenne pepper, and black pepper. Cook until fragrant, about 30 seconds. Stir in the beans and 9 cups water. Bring to boil over high heat. Reduce heat to medium-low and simmer vigorously, stirring occasionally, until beans are soft and liquid starts to thicken, 45 to 60 minutes.