Anti-agglomerants (AAs) are surface active molecules widely used in the petroleum industry, among others. It is believed that AAs strongly adsorb onto the surface of hydrate particles to prevent the growth of clathrate hydrate within oil pipelines. Small changes in their molecular structures can strongly affect the thermodynamic and kinetic stability of the system as a whole. Here we employ molecular dynamics simulations to study the interplay between the modification of the molecular structure, rigidity and collective effects of AAs designed to prevent hydrate agglomeration under the conditions encountered in rocking cell experiments. The AAs are surface-active compounds with a complex hydrophilic head and three hydrophobic tails whose structural rigidity is enhanced with the attachment of an aromatic group. Extrapolating from our simulation results, we predict that the aromatic group can positively or negatively affect the performance of the AAs, depending on its location along the hydrophobic tail. Our approach is based on first quantifying the molecular mechanisms responsible for the macroscopic performance and then altering the AA molecular structure to amplify said molecular mechanisms. Although the mechanisms at play depend on the application, the methodology implemented could be applicable to other high-tech industries, where the agglomeration of small particles must be controlled.