Equilibrium structure of a dense trimesic acid monolayer on a homogeneous solid surface: from atomistic simulation to thermodynamics

A general methodology for determining the thermodynamic characteristics of rigid organic crystals on the atomistic level is presented. The proposed approach is based on a combination of grid interpolation of the precalculated intermolecular potential and kinetic Monte Carlo simulation of the gas-crystal system with an explicit interphase. The two-phase system is stabilized in a wide range of external parameters with an imposed external potential and damping field. The damping field reduces the intermolecular potential at the edges of the crystals and turns it off in the gas phase. To determine the thermodynamic characteristics of a crystal the conditions of equality of chemical potentials in coexisting phases are used. The intermolecular pairwise potential can be calculated on the atomistic or quantum level. In the kinetic Monte Carlo simulations, a grid interpolation of the precalculated potential is performed on each iteration of the algorithm. We have applied the approach to the thermodynamic analysis of a dense monolayer of trimesic acid on a homogeneous surface. The calculated free energy and entropy for the dense "superflower" and filled chicken-wire phases obey the Gibbs-Duhem equation, which confirms the thermodynamic consistency of our approach. Using the proposed approach, we have revealed that the dense "superflower" phase becomes metastable at zero pressure and 470-500 K. Under these conditions, the filled chicken-wire structure with partially released hexagonal cages is thermodynamically favourable. The proposed approach is a potentially universal tool for the thermodynamic analysis of crystals formed by "rigid" organic molecules of any complexity on the atomistic level.

Molecular simulation study of 3,4-dihydroxyphenylalanine in the context of underwater adhesive design

Adhesives that can stick to multiple surface types in underwater and high moisture conditions are critical for various applications such as marine coatings, sealants, and medical devices. The analysis of natural underwater adhesives shows that L-3,4-dihydroxyphenylalanine (DOPA) and functional amyloid nanostructures are key components that contribute to the adhesive powers of these natural glues. The combination of DOPA and amyloid-forming peptides into DOPA-amyloid(-forming peptide) conjugates provides a new approach to design generic underwater adhesives. However, it remains unclear how the DOPA monomers may interact with amyloid-forming peptides and how these interactions may influence the adhesive ability of the conjugates. In this paper, we investigate the behavior of DOPA monomers, (glycine-DOPA)₃ chains, and a KLVFFAE and DOPA-glycine chain conjugate in aqueous environments using molecular simulations. The DOPA monomers do not aggregate significantly at concentrations lower than 1.0M. Simulations of (glycine-DOPA)₃ chains in water were done to examine the intra-molecular interactions of the chain, wherein we found that there were unlikely to be interactions detrimental to the adhesion process. After combining the alternating DOPA-glycine chain with the amyloid-forming peptide KLVFFAE into a single chain conjugate, we then simulated the conjugate in water and saw the possibility of both intra-chain folding and no chain folding in the conjugate.

Fluorination as a route towards unlocking the hydrogen bond donor ability of phenolic compounds in self-assembled monolayers

Fluorination turns a prototypical diphenol into an effective hydrogen-bond-donating building block for the formation of 2D phenol–pyridine cocrystals.

Electrostatically Driven Guest Binding in Self-Assembled Molecular Network of Hexagonal Pyridine Macrocycle at the Liquid/Solid Interface: Symmetry Breaking Induced by Coadsorbed Solvent Molecules

We present here the construction of a self-assembled two-dimensional network at the liquid/solid interface using a hexagonal pyridine macrocycle which binds an organic cation in its intrinsic porous space by electrostatic interactions. For this purpose, a hexagonal pyridinylene-butadiynylene macrocycle (PyBM) having six octyloxymethyl groups, PyBM-C8, was synthesized. As guests, tropylium (Tr) tetrafluoroborate and trioxatriangulenium (TOTA) hexafluorophosphate were used. In this study, we focused on (i) the network patterns of PyBM-C8 which change in response to its concentration and (ii) the position of the guest immobilized in the porous space of the macrocycle. Scanning tunneling microscopy (STM) observations at the interface of 1,2,4-trichlorobenzene (TCB) and highly oriented pyrolytic graphite (HOPG) revealed that PyBM-C8 formed four different polymorphs, oblique, loose hexagonal, linear, and rectangular, depending on the solute concentration and annealing treatment. Solvent TCB molecules are likely coadsorbed to not only the intrinsically porous space of PyBM-C8 (internal TCB) but also the space outside of the macrocycle between its alkyl chains (external TCB) in most of the cases. Upon adding the guest cation, whereas small Tr was not visualized in the pore due to size mismatching, larger TOTA was clearly observed in each pore. In addition, based on high-resolution STM images of the rhombus packing pattern of PyBM-C8, we revealed experimentally that TOTA was placed at an off-center position of the deformed hexagonal macrocyclic core in the rhombus pattern. On the basis of the molecular mechanics calculations, we hypothesize that the off-center location of TOTA is due to deformation of the hexagonal macrocycle through interaction with two external TCB molecules located at opposite edges of the macrocyclic core. Symmetry breaking of the macrocyclic host framework induced by coadsorbed surrounding solvent molecules thus plays a significant role in host-guest complexation at the liquid/solid interface.

Molecular Dynamics Simulation Study of Adsorption of Bioinspired Oligomers on Alumina Surfaces

The adsorption of small oligomers on a model metal oxide surface was studied with atomistically detailed molecular dynamics simulations. The oligomers consisted of two different repeat units: a maleimide, which contains a catechol functional group as in the dopamine residue found in marine adhesive proteins, and a methyl acrylate. A hydroxylated alumina surface was used as the model metal oxide surface. Adsorption interactions were investigated in aqueous as well as anhydrous conditions. In anhydrous conditions, the model oligomers displayed strong adsorption interactions with the surface. However, in aqueous conditions, the adsorption interactions were significantly weakened because of the competition with the water molecules for adsorption sites near the surface. Catechol functional groups in the model oligomers were found to play an important role in adsorption interactions with the alumina surface via hydrogen bonds. However, diverse adsorption properties were observed depending on compositions and sequences of two different repeat units and self-aggregations, indicating that the hydrogen bonding capability of catechol groups is not the sole factor determining adsorption properties.

Ultrathin Monomolecular Films and Robust Assemblies Based on Cyclic Catechols

We introduce a newly designed catechol-based compound and its application for the preparation of homogeneous monomolecular layers as well as for robust assemblies on various substrates. The precisely defined cyclic catechol material (CyCat) was prepared from ortho-dimethoxybenzene in a phenolic resin-like synthesis and subsequent deprotection, featuring molecules with up to 32 catechol units. The CyCat's chemical structure was carefully assessed via matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF), proton nuclear magnetic resonance (¹H NMR), diffusion ordered spectroscopy (2D DOSY) and high resolution electrospray ionization mass spectrometry (ESI MS) experiments. The formation of colloidal aggregates of the CyCat material in alkaline solution was followed by dynamic light scattering (DLS) and further verified by dropcasting CyCat from solution on highly oriented pyrolytic graphite (HOPG), which was examined by Kelvin probe force microscopy (KPFM). The adsorption behavior of the CyCat to form monomolecular layers was investigated in real time by surface plasmon resonance (SPR). Formation of these thin CyCat layers (1.6-2.1 nm) on Au, SiO₂ and TiO₂ substrates was corroborated by spectroscopic ellipsometry (SE) and X-ray photoelectron spectroscopy (XPS). The prepared coating perfectly reflects the surface structure of the underlying substrate and does not exhibit CyCat colloidal aggregates as verified by atomic force microscopy (AFM). The functional nature of the prepared catechol monolayers was evidenced by reaction with 4-bromophenethylamine and bis(3-aminopropyl)-terminated poly(ethylene oxide) (PEO). Multilayer assemblies were prepared by a simple procedure of iterative immersion in solutions of CyCat and a multifunctional amine on Au, SiO₂ and TiO₂ substrates forming thicker coatings (up to 12 nm). Postmodification with small organic molecules was performed to covalently attach trifluoroacetyl, tetrazole and 2-bromo-2-methylpropanoyl moieties to the amine groups of the multilayer assembly coating. Furthermore, the versatility of the novel multilayer coating was underpinned by "grafting-to" of phenacyl sulfide-terminated PEO and "grafting-from" of poly(methyl methacrylate) via surface-initiated atom transfer radical polymerization (ATRP).

Predicting supramolecular self-assembly on reconstructed metal surfaces

The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern.

Solvent-dependent stabilization of metastable monolayer polymorphs at the liquid-solid interface

Self-assembly of 1,3,5-tris(4'-biphenyl-4"-carbonitrile)benzene monolayers was studied at the liquid-solid interface by scanning tunneling microscopy. Application of different fatty acid homologues as solvents revealed a solvent-induced polymorphism. Yet, tempering triggered irreversible phase transitions of the initially self-assembled monolayers, thereby indicating their metastability. Interestingly, in either case, the same thermodynamically more stable and more densely packed monolayer polymorph was obtained after thermal treatment, irrespective of the initial structure. Again, the same densely packed structure was obtained in complementary solvent-free experiments conducted under ultrahigh vacuum conditions. Thus, self-assembly of metastable polymorphs at room temperature is explained by adsorption of partially solvated species under kinetic control. The irreversible phase transitions are induced by thermal desolvation, that is, desorption of coadsorbed solvent molecules.

Temperature-induced structural phase transitions in a two-dimensional self-assembled network

Two-dimensional (2D) supramolecular self-assembly at liquid-solid interfaces is a thermodynamically complex process producing a variety of structures. The formation of multiple network morphologies from the same molecular building blocks is a common occurrence. We use scanning tunnelling microscopy (STM) to investigate a structural phase transition between a densely packed and a porous phase of an alkylated dehydrobenzo[12]annulene (DBA) derivative physisorbed at a solvent-graphite interface. The influence of temperature and concentration are studied and the results combined using a thermodynamic model to measure enthalpy and entropy changes associated with the transition. These experimental results are compared to corresponding values obtained from simulations and theoretical calculations. This comparison highlights the importance of considering the solvent when modeling porous self-assembled networks. The results also demonstrate the power of using structural phase transitions to study the thermodynamics of these systems and will have implications for the development of predictive models for 2D self-assembly.