Since Murray et al. first synthesized monodisperse CdE (E = S, Se, Te) nanocrystals (NCs) using the hot injection method in 1993, significant advancements in colloidal chemistry over the past 30 years have enabled precise control over the size, shape, and monodispersity of various NC types, including metals, semiconductors from groups IV, 7 II-VI, IV-VI, and perovskites. As a result, NCs as ideal nanoscale building blocks for bottom-up self-assembly strategies. Self-assembly of colloidal NCs has emerged as a cost-effective and straightforward approach for materials design and device integration, enabling the fabrication of large-area flexible optoelectronic devices, such as solar cells, transistors, photodetectors, and light-emitting diodes. The concept of using NCs as "artificial atoms" to construct "artificial crystals" has led to successful assembly of NC superlattices with atomic-scale long-range order and fabrication of macroscopic materials on the centimeter scale, driven by innovations in surface engineering and self-assembly techniques. While NC assembly enables the formation of intricate nanoscale architectures, further exploration and practical application of these materials require a deeper understanding of interparticle interactions to achieve precise control over both micro-and macroscale structures. With rapid advances in colloidal NC synthesis and assembly techniques, there has been growing insight into their assembly mechanisms. Initially, the DLVO theory was applied to explain the self-assembly behavior of nonpolar colloidal NCs, suggesting that interparticle interactions are governed by a balance of core-core van der Waals attraction and steric effects from the organic ligand layers. According to this model, the primary driving force for colloidal NC assembly is van der Waals interactions between inorganic NC cores. However, for NCs with diameters smaller than 10 nm, calculations have shown that the interparticle attractions are less than 1 k B T , insufficient to explain the experimentally observed aggregation and assembly phenomena. Pioneering molecular simulation studies have shown that interactions between surface ligands play a dominant role in the self-assembly process. For example, Widmer-Cooper and Geissler, through explicit solvent Molecular Dynamics (MD) simulations, demonstrated that alkane chain ligands can crystallize into bundles even in good solvents, leading to strong interparticle attractions. As a result, it is now widely accepted that the surface chemistry strongly dictates the assembly dynamics of small-size spherical colloidal NCs. Recent studies suggest that even small adjustments to a colloidal NC system can induce significant changes in assembly dynamics, primarily through altered ligand-ligand interactions. In the case of saturated alkyl chain ligands, factors such as NC size, 26 ligand length, and solvent can influence the structure and interactions of surface ligands in solution. Moreover, subtle variations in ligand structure, such as the presence of a single carbon-carbon double bond, can drastically alter the ligand shell structure and significantly impact colloidal stability. Peng et al. proposed that ligands with branched or mixed-length alkyl chains increase intramolecular entropy, enhancing NC solubility in solution. However, due to challenges in synthesis, toxicity, and cost, only a limited set of nonpolar ligands (e.g., alkyl thiols, alkyl amines, and fatty acids) are commonly used in experiments for synthesizing and dispersing colloidal NCs. Furthermore, due to difficulties in experimental characterization, the structures of ligand shells and their effects on interparticle interactions remain poorly understood. To achieve precise control over colloidal NC interactions and assembly dynamics, it is crucial to develop a comprehensive ligand-solvent library that facilitates rational design across diverse ligands. In this study, we employ molecular simulations to investigate the structures of various nonpolar ligands on NC surfaces in solution and their resulting interparticle interactions. Using a model system of ∼5 nm PbSe NCs in hexane, we constructed a ligand library of 28 ligands with four distinct molecular fragments and functional groups, based on an 18-carbon hydrocarbon tail. Large-scale explicit-solvent MD simulations with enhanced sampling methods are employed to examine ligand packing on NC surfaces and the resulting interparticle interactions, with the aim of designing strategies to modulate interparticle attraction. This systematic investigation provides valuable simulation data and theoretical insights into the surface chemistry and self-assembly mechanisms of nonpolar colloidal NC systems.