Hypothesis The contact line pinning that appears in a flow coating process over substrates patterned with chemical or physical heterogeneities has been recently applied to deposit micro- and nanoparticles with great precision. However, the mechanism underlying pinning of a receding contact line at the nanoscale is not yet well understood. In the case of a contact line pinned at a chemical heterogeneity, we hypothesise that it is possible to establish a relation between the pinning time, the contact line velocity and the liquid/plate/heterogeneity affinity that can help to optimize particle deposition. Methods We use large-scale molecular dynamic (MD) simulations of a finite liquid bridge formed between two parallel, non–identical, smooth solid plates. The top plate slides relative to the bottom plate inducing a displacement of the four different contact lines of the liquid bridge. The introduction of a chemical heterogeneity on the bottom plate by modifying locally the liquid–solid affinity provokes the transient pinning of the contact line in contact with the bottom substrate. By means of this simple MD simulation, we can study the mechanism of contact line pinning and its relation with the liquid/heterogeneity affinity and the contact line velocity. Additionally, we compare this mechanism with the case of the receding contact line pinned on a physical heterogeneity (a simple step discontinuity). Findings We propose an analytical model that predicts the values of the dynamic contact angles in the general case of a capillary liquid bridge confined between two parallel plates with different wettabilities versus the relative velocity of the top plate. These predictions are successfully validated by the results of the large–scale MD simulations. The model allows thus to predict the value of the dynamic contact angles for the different contact lines of the system versus the relative speed of the moving plate. Once the chemical heterogeneity is introduced in the bottom plate, we show that when the receding contact line reaches the patch it remains temporarily pinned while the receding contact angle evolves with time. Once the receding angle reaches the value of the equilibrium contact angle of the patch, the receding contact line overcomes pinning. A geometrical model able to predict the pinning time is proposed and validated by our MD simulations. The pinning time depends not only on the relative plate velocity and plate wettability properties but also on the separation distance between the plates confining the capillary bridge. The model can consequently be used to select the substrate wettability or meniscus geometry suitable to impose the pinning time required for specific applications.@en