Understanding how chemical modifications alter the atomic-scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and non-covalent interactions in designing crystals while piggybacking on the driving force of molecular self-assembly has augmented our efforts to understand the emergence of complex structures using directed synthesis. Here, we prepared microcrystalline powders of the silver 2-, 3-, and 4-fluorobenzenethiolates and resolved their structures by small molecule serial femtosecond X-ray crystallography (smSFX). These three compounds enable us to examine the emergence and role of supramolecular synthons in the crystal structures of three-dimensional metal-organic chalcogenolates (MOChas). The unique divergence in their optoelectronic, morphological, and structural behavior was assessed. The extent of C-H···F interactions and their influence on the structure and the observed trends in the thermal stability of the crystals were quantified through theoretical calculations and thermogravimetric analysis.