Ordering of monomers, dimers and polymers of deposited BrIPy molecules: a modeling study.

We propose a lattice model describing the ordering of 1,6-dibromo-3,8-diiodopyrene (BrIPy) molecules on the Au(111) surface into two-dimensional structures and correlated one dimensional rows. Our model employs three (intact, singly and doubly deiodinated) types of BrIPy molecules and mimics the situation which occurs with increasing temperature, where the majority of intact molecules form ordered two-dimensional networks, while most of the doubly deiodinated molecules assemble into long organometallic polymeric rows. We use DFT calculations to determine the values of intermolecular interactions for intact molecules and propose a strategy for estimating the interactions for deiodinated molecules, where the organometallic interaction with Au atoms plays the dominant role.

Temperature-induced molecular reorganization on Au(111) driven by oligomeric defects.

The formation of ordered molecular structures on surfaces is determined by the balance between molecule-molecule and molecule-substrate interactions. Whether the aggregation process is guided by non-covalent forces or on-surface reactions, a deeper understanding of these interactions is pivotal to formulating a priori predictions of the final structural features and the development of bottom-up fabrication protocols. Theoretical models of molecular systems corroborate the information gathered through experimental observations and help explain the thermodynamic factors that underpin on-surface phase transitions.

Self-assembly of 5,6-dihydroxyindole-2-carboxylic acid: polymorphism of a eumelanin building block on Au(111).

Investigating two-dimensional (2D) self-assembled structures of biological monomers governed by intermolecular interactions is a prerequisite to understand the self-assembly of more complex biomolecular systems. 5,6-Dihydroxyindole carboxylic acid (DHICA) is one of the building blocks of eumelanin - an irregular heteropolymer and the most common form of melanin which has potential applications in organic electronics and bioelectronics. By means of scanning tunneling microscopy, density functional theory and Monte Carlo calculations, we investigate DHICA molecular configurations and interactions underlying the multiple 2D patterns formed on Au(111).

Room-temperature surface-assisted reactivity of a melanin precursor: silver metal-organic coordination versus covalent dimerization on gold.

The ability of catecholamines to undergo oxidative self-polymerization provides an attractive route for preparation of coatings for biotechnology and biomedicine applications. However, efforts toward developing a complete understanding of the mechanism that underpins polymerization have been hindered by the multiple catechol crosslinking reaction pathways that occur during the reaction. Scanning tunneling microscopy allows the investigation of small molecules in a reduced-complexity environment, providing important insight into how the intermolecular forces drive the formation of supramolecular assemblies in a controlled setting.