We start by studying the little investigated structure of singly deprotonated alkanedithiols on single flat gold surfaces. In the next step, we add a second gold surface to the structure to build a sandwich structure that resembles the interface of GNP assemblies, and extract the preferred surface-to-surface distance. We compare this with experimental data from the literature. Additionally, we measure interparticle distances of 1,9-nonanedithiol (9DT) cross-linked GNP assemblies with larger GNP diameters using grazing-incidence small-angle X-ray scattering (GISAXS) to study the impact of the particle size and curvature onto the interparticle distance, and to generate reference data that is closer in curvature (or lack thereof) to our simulated flat gold surfaces. We show the potential of limiting the GNP film structure to single, flat, particle-particle interfaces, as well as constraints. We also point out limitations of the reactive force field, which was parameterized for monothiolates, when dealing with alkanedithiolate ligands. In addition, electron transport calculations are performed to correlate structural and electrical properties of the systems and, again, compared with experimental data.