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. Here, we report a scanning tunneling microscopy investigation of a tribromo-substituted heterotriangulene on the Au(111) surface, which initially forms an extended close-packed ordered structure stabilized by BrBr halogen bonds when deposited at room temperature. X-ray photoelectron spectroscopy reveals that annealing the self-assembled layer induces a fraction of the molecular precursors to partially dehalogenate that in turn leads to the formation of a less stable BrO non-covalent network which coexists with the short oligomers. Density functional theory (DFT) and Monte Carlo (MC) simulations illustrate how dimer moieties act as defects whose steric hindrance prevents the retention of the more stable configuration. A small number of dimers is sufficient to drive the molecular reorganization into a lower cohesive energy phase. Our study shows the importance of a combined DFT - MC approach to understand the evolution of molecular systems on substrates.

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). While DHICA self-assembled molecular networks (SAMNs) are dominated by the hydrogen bonding of carboxylic acid dimers, a variety of 2D architectures are formed due to the multiple weak interactions of the catechol group. The hydroxyl group also allows for redox reactions, caused by oxidation via O2 exposure, resulting in molecular rearrangement. The susceptibility of the molecules to oxidation is affected by their SAMNs architectures, giving insights on the reactivity of indoles as well as highlighting non-covalent assembly as an approach to guide selective oxidation reactions.

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. Capitalizing on this approach, we studied the self-assembly of 5,6-dihydroxy-indole (DHI) on Au(111) and Ag(111) to investigate the interactions that affect the two-dimensional growth mechanism and to elucidate the behavior of the catechol group on these two surfaces. X-ray photoelectron spectroscopy, together with density functional theory and Monte Carlo modeling, helps unravel the differences between the two systems. The molecules form large ordered domains, yet with completely different architectures. Our data reveal that some of the DHI molecules deposited on Ag are in a modified redox state, with their catechol group oxidized into quinone. On Ag(111), the molecules are deposited in long-range lamellar patterns stabilized by metal-organic coordination, while covalent dimer pairs are observed on Au(111). We also show that the oxidation susceptibility is affected by the substrate, with the DHI/Au remaining inert even after being exposed to O2 gas.

Phase transition properties of the Bell-Lavis model.

Using Monte Carlo calculations we analyze the order and the universality class of phase transitions into a low-density (honeycomb) phase of a triangular antiferromagnetic three-state Bell-Lavis model. The results are obtained in a whole interval of chemical potential µ corresponding to the honeycomb phase. Our results demonstrate that the phase transitions might be attributed to the three-state Potts universality class for all µ values except for the edges of the honeycomb phase existence. At the honeycomb phase and the low-density gas phase boundary the transitions become of the first order. At another, honeycomb-to-frustrated phase boundary, we observe the approach to the crossover from the three-state Potts to the Ising model universality class. We also obtain the Schottky anomaly in the specific heat close to this edge. We show that the intermediate planar phase, found in a very similar antiferromagnetic triangular Blume-Capel model, does not occur in the Bell-Lavis model.

Antiferromagnetic triangular Blume-Capel model with hard-core exclusions.

Using Monte Carlo simulation, we analyze phase transitions of two antiferromagnetic (AFM) triangular Blume-Capel (BC) models with AFM interactions between third-nearest neighbors. One model has hard-core exclusions between the nearest-neighbor (1NN) particles (3NN1 model) and the other has them between the nearest-neighbor and next-nearest-neighbor particles (3NN12 model). Finite-size scaling analysis reveals that in these models, the transition from the paramagnetic to long-range order (LRO) AFM phase is either of the first order or goes through an intermediate phase which might be attributed to the Berezinskii-Kosterlitz-Thouless (BKT) type. The properties of the low-temperature phase transition to the AFM phase of the 1NN, 3NN1, and 3NN12 models are found to be very similar for almost all values of a normalized single-ion anisotropy parameter, 0 < δ < 1.5. Higher temperature behavior of the 3NN12 and 3NN1 models is rather different from that of the 1NN model. Three phase transitions are observed for the 3NN12 model: from the paramagnetic phase to the phase with domains of the LRO AFM phase at T(c), from this structure to the diluted frustrated BKT-type phase at T(2), and from the frustrated phase to the AFM LRO phase at T(1). For the 3NN12 model, T(c) > T(2) > T(1) at 0 < δ < 1.15 (range I), T(c) ≈ T(2) > T(1) at 1.15 < δ < 1.3 (range II), and T(c) = T(2) = T(1) at 1.3 < δ < 1.5 (range III). For the 3NN1 model, T(c) ≈ T(2) > T(1) at 0 < δ < 1.2 (range II) and T(c) = T(2) = T(1) at 1.2 < δ < 1.5 (range III). There is only one first-order phase transition in range III. The transition at T(c) is of the first order in range II and either of a weak first order or a second order in range I.

A model of melamine molecules ordering on metal surfaces.

The model of melamine molecules ordering into planar honeycomb and closed packed phases is proposed. To account for the "side-to-side" melamine-melamine molecular interactions, we use the version of the antiferromagnetic Blume-Capel model with some exclusions. The model is solved by Monte Carlo calculations on a triangular lattice, a slightly rescaled version of Au(111) and Ag(111) lattices on which the main experimental data are obtained. The ordered phases are formed when mutual distance between the centers of molecules is within sixth and seventh nearest neighbor distances of rescaled substrate lattice. We obtain the ground state phase diagram with honeycomb and three closed-packed phases and density-temperature phase diagram with three pure phases (gas, honeycomb, and close-packed) and their two-phase coexistences.

Pin-wheel hexagons: a model for anthraquinone ordering on Cu(111).

The 4-state model of anthraquinone molecules ordering in a pin-wheel large-pore honeycomb phase on Cu(111) is proposed and solved by Monte Carlo simulation. The model is defined on a rescaled triangular lattice with the lattice constant a being equal to intermolecular distance in the honeycomb phase. The pin-wheel triangle formations are obtained taking into account the elongated shape of the molecules and anisotropic interactions for main two attractive short range (double and single dimeric) H-bond interactions. The long-range intermolecular interactions, corresponding to repulsive dipole-dipole forces, are assumed to be isotropic. Also, a very small (compared to short-range forces) isotropic attractive long-range interaction at the "characteristic" distance of a pore diameter is employed, and its effect carefully studied. This interaction is crucial for a formation of closed porous ordered systems, pin-wheel hexagons in particular. If each side of a pin-wheel hexagon is formed of n parallel molecules, the distance of this characteristic interaction is a√(3n(2)+1). The phase diagrams including different pin-wheel hexagon phases and a variety of other ordered structures are obtained. By changing the distance of characteristic interaction, different ordering routes into the experimental pin-wheel honeycomb phase are explored. The results obtained imply that classical explanation of the origin of the pin-wheel honeycomb phase in terms of some balance of attractive and repulsive forces cannot be totally discounted yet.

Statistical model for self-assembly of trimesic acid molecules into homologous series of flower phases.

The statistical three-state model is proposed to describe the ordering of triangular TMA molecules into flower phases. The model is solved on a rescaled triangular lattice, assuming following intermolecular interactions: exclusion of any molecules on nearest neighbor sites, triangular trio H-bonding interactions for molecules of the same orientation on next-nearest neighbor sites, and dimeric H-bonding interactions for molecules of different ("tip-to-tip") orientations on third-nearest neighbor sites. The model allows us to obtain the analytical solution for the ground state phase diagram with all homologous series of flower phases included, starting with the honeycomb phase (n=1) and ending with the superflower structure (n=∞). Monte Carlo simulations are used to obtain the thermodynamical properties of this model. It is found that phase transitions from disordered to any of the flower phases (except n=1) undergo via intermediate correlated triangular domains structure. The transition from the disordered phase to the intermediate phase is, most likely, of the first order, while the transition from the intermediate to the flower phase is definitely first order phase transition. The phase diagrams including low-temperature flower phases are obtained. The origin of the intermediate phase, phase separation, and metastable structures are discussed.

Ordered assemblies of triangular-shaped molecules with strongly interacting vertices: phase diagrams for honeycomb and zigzag structures on triangular lattice.

The model for ordering of triangular-shaped molecules with strongly interacting vertices is proposed and solved by the Monte Carlo method. The model accounts for three main intermolecular interactions and three states (two main orientations and a vacancy state) of a molecule on triangular lattice, the situation which is encountered in self-assembly of TMA molecules characterized by strongly directional H-bonding. Distinguishing the main "tip-to-tip" interaction, we calculate the phase diagrams for the honeycomb and frustrated honeycomb structures and demonstrate how these structures shrink and vanish with gradual increase of two other ("side-to-side" and "tip-to-side") interactions. We study the effect of frustration on the phase diagram, since the frustrated phase is obtained at the Ising limit of the model. We also demonstrate how the inclusion of longer-range interactions leads to substitution of the frustrated phase by the zigzag structure. Finally, we obtain the phase diagram with two experimentally found TMA structures (honeycomb and zigzag) and discuss the conditions of their existence by comparison with the experimental results.

Phase diagram of subphtalocyanine ordering on Ag(111).

A model of subphtalocyanine molecules ordering on Ag(111) is proposed. We have demonstrated that the driving force of the ordering into honeycomb and hexagonal close packed patterns is a balance of intermolecular and subphtalocyanine-Ag interactions which can be generally expressed by a potential with infinite exclusion in a sufficiently large number of nearest coordination spheres of Ag(111) lattice and oscillatingly decaying behavior outside the sphere of exclusion. To cope with computational problems due to large size of the molecules compared to the substrate lattice period, we introduce the rescaling of Ag(111) lattice, and took into account an infinite exclusion of first, second, and third neighbors, attraction-of fourth and fifth, and repulsion-of sixth and seventh. The phase diagram is obtained by the lattice gas model using Monte Carlo simulations. Very strong first order phase transitions, causing the two-phase coexistence, were found between disordered and honeycomb as well as between disordered and hexagonal closed packed phases.