The formation of
defect-free two-dimensional nanocrystal (NC) superstructures
remains a challenge as persistent defects hinder charge delocalization
and related device performance. Understanding defect formation is
an important step toward developing strategies to mitigate their formation.
However, specific mechanisms of defect formation are difficult to
determine, as superlattice phase transformations that occur during
fabrication are quite complex and there are a variety of factors influencing
the disorder in the final structure. Here, we use Molecular Dynamics
(MD) and electron microscopy in concert to investigate the nucleation
of the epitaxial attachment of lead chalcogenide (PbX, where X = S,
Se) NC assemblies. We use an updated implementation of an existing
reactive force field in an MD framework to investigate how initial
orientational (mis)alignment of the constituent building blocks impacts
the final structure of the epitaxially connected superlattice. This
Simple Molecular Reactive Force Field (SMRFF) captures both short-range
covalent forces and long-range electrostatic forces and allows us
to follow orientational and translational changes of NCs during superlattice
transformation. Our simulations reveal how robust the oriented attachment
is with regard to the initial configuration of the NCs, measuring
its sensitivity to both in-plane and out-of-plane misorientation.
We show that oriented attachment nucleates through the initial formation
of dimers, which corroborate experimentally observed structures. We
present high-resolution structural analysis of dimers at early stages
of the superlattice transformation and rationalize their contribution
to the formation of defects in the final superlattice. Collectively,
the simulations and experiments presented in this paper provide insights
into the nucleation of NC oriented attachment, the impact of the initial
configuration of NCs on the structural fidelity of the final epitaxially
connected superlattice, and the propensity to form commonly observed
defects, such as missing bridges and atomic misalignment in the superlattice
due to the formation of dimers. We present potential strategies to
mitigate the formation of superlattice defects.