The hexanucleotide repeat expansion GGGGCC (G4C2) in the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The transcribed RNA self-assembles into multi-chain quaternary structures through multivalent base pairing, and this assembly behavior constitutes the molecular basis for pathological liquid-liquid phase separation and the formation of pathological condensates. Here, using all-atom molecular dynamics simulations, we investigate how terahertz (THz) frequencies modulate the physical coupling between interchain contacts and the solvent interface in a five-chain 5xG4C2 RNA assembly. Under a field strength of 0.5 V/nm, seven distinct frequencies spanning 0-37.3 THz were examined, each with 20 independent 200-ns replicates. Four structural parameters covering two orthogonal dimensions, interchain contacts and the solvent interface, were analyzed using Student’s t-test, three linear displacement models, and bootstrap resampling (1000 iterations). Across the entire frequency range, neither the interchain hydrogen-bond network nor backbone stacking was significantly affected. In contrast, solvent-accessible surface area (SASA) exhibited a marked frequency-selective decrease, whereas the number of interfacial water molecules dropped only at the frequency of maximal compaction (3.0 THz), indicating that compaction is not simply due to interfacial water expulsion. Linear permutation model analysis revealed a cooperative switch at 11.9 THz, where the signs of three core coefficients flipped simultaneously and the coefficient of determination rose sharply, demonstrating that interchain contacts become effective drivers of surface burial and water release. At 20.5 THz, the compactness-driven water-release channel was selectively activated; this channel subsided at 32.2 THz, where a hydrogen-bond-driven channel began to emerge, and became fully activated at 37.3 THz. Interfacial hydration density showed no statistically significant change at any frequency, and global regression confirmed that changes in interfacial water are dominated by SASA compression rather than altered surface chemical affinity. Collectively, these findings establish that THz frequency provides a continuously tunable means of resolving interactions within the assembly: different frequencies selectively elicit responses along distinct physical dimensions, mechanical compaction, cooperative switching of surface burial and water-release efficiency, and channel-selective activation, while the interfacial hydration density remains conserved. This frequency-encoding framework offers a physical basis for understanding terahertz-nucleic-acid supramolecular interactions at the molecular level.