Self-assembly at surfaces

Molecular self-assembly of surface-confined architectures attracted significant attention for their promising applications in the fields of surface patterning, host-guest chemistry, molecular electronics and spintronics, and as catalytic model systems. Here, the long-range ordered networks are formed on surfaces from elementary building blocks: organic molecules and metal atoms. The proper design of molecular building units and selection of metal atoms enables the engineering of extended 2D structures bearing the desired functionality.​

Phase Transformations

​Low-energy electron microscopy (LEEM) is a surface-science method that enables mesoscopic surface imaging in real-time. We have employed real-time LEEM to visualize a phase transformation induced by the carboxylation of 4,4’ biphenyl dicarboxylic acid (BDA) on Ag(001) under ultra-high vacuum conditions. In the combination with kinetic Monte Carlo simulations, we reveal that the phase transformation exhibits a rich variety of phenomena. Some of them are common also for inorganic phases like Ostwald ripening. The other, the burst nucleation of the new phase is a characteristic of the molecular islands at surfaces that are close to the thermodynamic equilibrium. 

P. Procházka, et al.: Multiscale Analysis of Phase Transformations in Self-Assembled Layers of 4,4’-Biphenyl Dicarboxylic Acid on the Ag(001) Surface, ACS Nano 14 (2020), 7269.

Full Layer​ Transformation

BDA molecules comprise two carboxyl groups, which can be thermally deprotonated at Ag(001) surface. As these groups are negatively charged the molecular structure should be changed and molecular phases irreversibly transform into different ones.  In the full molecular layer covering the entire surface, the phase transformation proceeds differently from sub-monolayer coverages. There no space to grow phases with a lower density and molecules cannot diffuse or reorient. As a result new, compressed, phases are formed if possible.  If not, the excessive molecules are expelled making space for the standard sub-monolayer phases. 

​P. Procházka, L. Kormoš, A. Shahsavar, V. Stará, A. O. Makoveev, T. Skála, M. Blatnik, J. Čechal: Phase Transformations in a Complete Monolayer of 4,4’-Biphenyl-Dicarboxylic Acid on Ag(001). Appl. Surf. Sci. 547, (2021), 149115. ​

k-Uniform Tiling​

Tilings are the mathematical concept that enables to describe tesselation of the plane into polygons. We have shown that k-uniform tilings comprising several distinct tiles can be prepared from differently deprotonated biphenyl dicarboxylic acid (BDA) molecules. These are obtained by their controlled chemical transformation on the Ag(001) surface. The partially deprotonated BDA mediates the seamless connection of two distinct binding motifs in a single long-range ordered molecular phase and thus enables the connection of distinct tiles together resulting in the realization of 2- and 3-uniform tilings.                                           

L. Kormoš, P. Procházka, A.O. Makoveev, J. Čechal, Nat. Commun. 11 (2020), 1856.                           

Step Edge Passivation

Our model molecule, BDA, is almost instantly deprotonated at the Cu (001) surface. The deprotonated groups are strongly interacting with the substrate and even more with the step-edge atoms; this results in step-edge decoration by BDAs. As the other side of BDA is also deprotonated, the densely arranged carboxylates will prevent attachment of any further BDA's causing an effective step edge passivation. This limits the BDA diffusion over the step edges and the attachment of additional BDA molecules preventing nucleation and growth of molecular islands on the step edges. 

L. Kormoš, P. Procházka, T. Šikola, J. Čechal, J. Phys. Chem. C 122 (2018), 2815.