Metal-Organic Frameworks (MOFs) constitute a class of porous materials that thanks to their high porosity and surface area, have ignited interest in a plethora of applications including carbon capture and storage , separations 3 , extraction of water from air , electrodes and drug delivery . Nevertheless, the stability of MOFs is lower than other porous materials and their scale-up is still problematic, thus reducing their applicability . The presence of defects in MOFs is known to affect their thermomechanical properties, stability, synthesis costs, and overall suitability for industrial applications . This led recent efforts to understand the detailed mechanisms associated with MOF synthesis in order to regulate the extent of defects . The formation of secondary building units (SBUs) during the early stages of synthesis is crucial in determining the final properties of a MOF. Ferey et al. suggested a synthesis mechanism involving the formation of pre-nucleation building units (PNBUs) and their subsequent nucleation. These are soluble zero-charged species such as the half-SBUs mentioned in this work. More experimental works have identified PNBUs and evaluated their role in the final MOF structure following the approach of synthesis through SBU formation . Recently, Liu et al. suggested a three-step MOF nucleation mechanism through a mixed experimental and computational work. They identified metastable structures that recrystallize into the MOF, hence acting as precursors to the nucleation of crystalline MOFs, but could not elucidate the molecular mechanisms governing the process. It has been observed that the composition of the synthesis mixture affects the thermodynamics and kinetics of MOF nucleation and growth . Ions are known to promote MOF crystallinity , while their concentration needs to be finetuned in order to achieve this . At last, we should note that fluoride anions were considered in this work following the original MIL-101(Cr) synthesis but fluoride-free synthetic routes also exist . Also, MOF synthesis optimization is very important in order to manufacture MOFs for different applications . Additionally, manufacturing cost can be decreased by optimizing the synthetic process (e.g., processing time, pressure, and temperature) . Optimization is often difficult due to the several possibilities of metal-ligand combinations and the large number of phases emerging for each one . Consequently, isoreticular modification of a well-known MOF by exchanging ligands while maintaining metal-ligand connec-tivity is ordinarily employed to study new MOFs for a particular application . At last, electronic structure parameters can be optimized through mixing different metals in a MOF . Computational studies on the early stages MOF self-assembly are rather limited . Yoneya et al. studied MOF self-assembly with a focus on optimizing simulation parameters using dummy atoms in implicit solvent. Biswal and Kusalik have studied MOF self-assembly using Langevin dynamics, and their results imply the existence of several local energy minima associated with the process. Wells et al. investigated the early stages of MOF synthesis using Monte Carlo methods and developed an algorithm able to distinguish between different phases with respect to composition. Colon et al. focused on the self-assembly of MOF-5 using enhanced sampling methods, but they did not consider all relevant metastable states as they restrained the endpoints of the biased simulation. Cantu et al. investigated the assembly of MIL-101(Cr) building blocks at the density functional theory level, and identified possible SBU isomers through modelling the kinetics of their formation. Finally, the formation of "metal-free" covalent organic frameworks has been studied using coarse-grained models for building blocks . The shape and structure of clusters can be examined as a means to characterize the growth of complex materials. In this respect, the fractal dimension is a well-known descriptor of compactness used to describe the self-assembly of metal-ligand systems . Recently, new synthetic strategies to form self-similar MOFs that exhibit fractal geometry were suggested . Maurer et al. observed that fractal dimension provides useful insight into the spatial arrangement of structures with similar radii of gyration. Tsao et al. used fractal dimension to explore the potential of hydrogen storage inside MOF pores. Goesten et al. investigated MOF growth through characterizing the fractal nature of precursors. At last, Liu et al. linked the shape of clusters with crystallinity during MOF nucleation. Graph theory has been used to model nucleation of metaloxide compounds , or construction of molecular polyhedra . Also, it has been successfully applied to study the properties of metal-ligand systems and MOFs , and characterize the dynamic behavior of functional materials . In a previous work, we have demonstrated how the initial population of isomer half-SBUs, choice of solvent, and ionic strength affect the thermodynamics of defect formation based on interactions between couples of half-SBUs . There, we computed free energy landscapes and evaluated the equilibrium population of stable and meta-stable, crystal-like and noncrystal-like dimers formed from half-SBUs. We concluded that in absence of ions, half-SBUs form entropically controlled defects 57 , while ions tend to control the conformational landscape of dimers, by hindering ligand rotation that may lead to defects as a result of 𝜋 -𝜋 stacking of the phenyl rings. The latter dominate the equilibrium probability of dimers in the absence of ions. Consequently, interactions between ions and half-SBUs increase the equilibrium probability of crystal-like units.