We report an experimental investigation of the role of molecular-level interactions in determining the anchoring of liquid crystals supported on surfaces possessing nanometer-scale topography on which immunoglobulins (IgG) are specifically bound to immobilized antigens. Molecular-level interactions are manipulated by using self-assembled monolayers (SAMs) of organosulfur compounds formed on thin films of gold that possess an anisotropic, nanometer-scale topography (corrugation). We compare the orientational response of liquid crystal to the presence of anti-biotin IgG specifically bound to mixed SAMs formed from biotin-(CH2)(2)[(CH2)(2)O](2)NHCO(CH2)(11)SH and either CH3(CH2)(6)SH or CH3(CH2)(7)SH on the gold films. When using SAMs that contain 70% alkanethiolate, we measure the orientational (and thus optical) response of the liquid crystal to IgG to depend on whether the alkanethiolate within the mixed SAM is CH3(CH2)(6)S or CH3(CH2)(7)S. We conclude, therefore, that molecular-level interactions controlled by the structure of the alkanethiolates, in addition to long-range (elastic) interactions that result from the nanometer-scale topography of the gold film, influence the response of liquid crystal to the IgG specifically bound to these surfaces. The influence of the nanometer-scale topography does, however, dominate the response of the liquid crystal. The molecular interactions appear to influence the lifetimes of line defects formed as nematic phases spread across these surfaces: the defects are observed to anneal quickly (similar to seconds) on SAMs containing CH3(CH2)(7)S but slowly (> days) on those containing CH3(CH2)(6)S. The pinning of defects within the liquid crystal when using SAMs containing CH3(CH2)(6)S causes these surfaces to be more sensitive to bound IgG than surfaces containing CH3(CH2)(7)S.