In this paper, we propose a mixed integer program (MIP) formulation which can be used to synthesize multi-loop hierarchical control structures for tightly energy integrated plants, which are known to exhibit multiple-time scale energy dynamics. First, we represent the network as an energy flow graph, and perform graph reduction using graph-theoretic algorithms that we have previously developed, to analyze the time scale properties of the network and obtain energy flow subgraphs for each time scale. Then, from each energy flow subgraph, we construct an equation graph from which we can extract relative degree information. Using the proposed MIP, optimal input/output pairing sets are obtained, which minimize the structural coupling in each time scale. We illustrate the application of the proposed work through a case study of a benchmark chemical process.