On-surface polymerization of functional organic molecules has been recently recognized as a promising route to persistent low-dimensional structures with tailorable properties. In this contribution, using the coarse-grained Monte Carlo simulation method, we study the initial stage of the Ullmann coupling of doubly halogenated chrysene isomers adsorbed on a catalytically active (111) crystalline surface. To that end, we focus on the formation of labile metal-organic precursor structures preceding the covalent bonding of chrysene monomers. Four monomeric chrysene units with differently distributed halogen substituents were probed in the simulations, and the resulting precursor structures were compared and quantified. Moreover, the effect of (pro)chirality of chrysene tectons on the structure formation was elucidated by running separate simulations in enantiopure and racemic systems. The calculations showed that suitable manipulation of the halogen substitution pattern allows for the creation of diverse precursor architectures, ranging from straight and winded chains to cyclic oligomers with enantiopure, racemic, and nonracemic composition. The obtained findings can be helpful in developing synthetic strategies for covalent polymers with predefined architecture and functionality.
Materials with disordered structures may exhibit interesting properties. Metal-organic frameworks (MOFs) are a class of hybrid materials composed of metal nodes and coordinating organic linkers. Recently, there has been growing interest in MOFs with structural disorder and the investigations of amorphous structures on surfaces. Herein, we demonstrate a bottom-up method to construct disordered molecular networks on metal surfaces by selecting two organic molecule linkers with the same symmetry but different sizes for preparing two-component samples with different stoichiometric ratios. The amorphous networks are directly imaged by scanning tunneling microscopy under ultrahigh vacuum with a submolecular resolution, allowing us to quantify its degree of disorder and other structural properties. Furthermore, we resort to molecular dynamics simulations to understand the formation of the amorphous metal-organic networks. The results may advance our understanding of the mechanism of formation of monolayer molecular networks with structural disorders, facilitating the design and exploration of amorphous MOF materials with intriguing properties.
The diversity of surface-confined metal-organic precursor structures, which recently have been observed experimentally, poses a question of how the individual properties of a molecular building block determine those of the resulting superstructure. To answer this question, we use the Monte Carlo simulation technique to model the self-assembly of metal-organic precursors that precede the covalent polymerization of halogenated PAH isomers. For this purpose, a few representative examples of low-dimensional constructs were studied, and their basic structural features were quantified using such descriptors as the orientational order parameter, radial distribution function, and one- and two-dimensional structure factors. The obtained results demonstrated that the morphology of the precursor (and thus the subsequent polymer) could be effectively tuned by a suitable choice of molecular parameters, including size, shape, and intramolecular distribution of halogen substituents. Moreover, our theoretical investigations showed the effect of the main structural features of the precursors on the related indirect characteristics of these constructs. The results reported herein can be helpful in the custom designing and characterization of low-dimensional polymers with adjustable properties.
Surface-assisted fabrication of molecular network architectures has been a promising route to low-dimensional materials with unique physicochemical properties and functionalities. One versatile way in this field is the Ullmann coupling reaction of halogenated organic monomers on catalytically active metallic surfaces. In this work, using the coarse-grained Monte Carlo simulations, we studied the on-surface self-assembly of metal-organic precursors preceding the covalent Ullman-type linkage of tetrahalogenated anthracene building blocks. To that end, a series of positional isomers was examined and classified with respect to their ability of creation of extended network structures. Our simulations focused on the identification of basic types of self-assembly scenarios distinguishing enantiopure and racemic systems and producing periodic and aperiodic networks. The calculations carried out for selected tectons demonstrated wide possibilities of controlling porosity (e. g. pore size, shape, periodicity, chirality, heterogeneity) of the networks by suitable functionalization of the monomeric unit. The findings reported herein can be helpful in rational designing of 2D polymeric networks with predefined structures and properties.
Organic synthesis reactions in the adsorbed phase have been recently an intensively studied topic in heterogeneous catalysis and material engineering. One of such processes is the Ullmann coupling in which halogenated organic monomers are transformed into covalently bonded polymeric structures. In this work, we use the lattice Monte Carlo simulation method to study the on-surface self-assembly of organometallic precursor architectures comprising tetrasubstituted naphthalene building blocks with differently distributed halogen atoms. In the coarse grained approach adopted herein the molecules and metal atoms were modeled by discrete segments, two connected and one, respectively, placed on a triangular lattice representing a (111) metallic surface. Our simulations focused on the influence of the intramolecular distribution of the substituents on the morphology of the resulting superstructures. Special attention was paid to the molecules that create porous networks characterized by long-range order. Moreover, the structural analysis of the assemblies comprising prochiral building blocks was made by running simulations for the corresponding enantiopure and racemic adsorbed systems. The obtained results demonstrated the possibility of directing the on-surface self-assembly towards networks with controllable pore shape and size. These findings can be helpful in designing covalently bonded 2D superstructures with predefined architecture and functions.
Ring/chain competition in oligomerization reactions represents a long-standing topic of synthetic chemistry and was treated extensively for solution reactions but is not well-understood for the two-dimensional confinement of surface reactions. Here, the kinetic and thermodynamic principles of ring/chain competition in on-surface synthesis are addressed by scanning tunneling microscopy, X-ray photoelectron spectroscopy, and Monte Carlo simulations applied to azulene-based organometallic oligomers on Cu(111). Analysis of experiments and simulations reveals how the ring/chain ratio can be controlled through variation of coverage and temperature. At room temperature, non-equilibrium conditions prevail and kinetic control leads to preferential formation of the entropically favored chains. In contrast, high-temperature equilibrium conditions are associated with thermodynamic control, resulting in increased yields of the energetically favored rings. The optimum conditions for ring formation include the lowest possible temperature within the regime of thermodynamic control and a low coverage. The general implications are discussed and compared to the solution case.
Directing the self-assembly of organic building blocks with 2D templates has been a promising method to create molecular superstructures having unique physicochemical properties. In this work the on-surface self-assembly of simple ditopic functional molecules confined inside periodic nanotemplates was modeled by means of the lattice Monte Carlo simulation method. Two types of confinement, that is honeycomb porous networks and parallel grooves of controlled diameter and width were used in the calculations. Additionally, the effect of (pro)chirality of the adsorbing molecules on the outcome of the templated self-assembly was examined. To that end, enantiopure and racemic assemblies were studied and the resulting structures were identified and classified. The obtained findings demonstrated that suitable tuning of the structural parameters of the templates enables directing the self-assembly towards linear and cyclic aggregates with controlled size. Moreover, chiral resolution of the molecular conformers using honeycomb networks with adjusted pore size was found possible. Our theoretical predictions can be helpful in designing structured surfaces to direct self-assembly and polymerization of organic functional building blocks.
Surface-confined self-assembly of functional molecular building blocks has recently been widely used to create low-dimensional, also covalent, superstructures with tailorable geometry and physicochemical properties. In this contribution, using the lattice Monte Carlo simulation method, we demonstrate how the structure-property relation can be established for the 2D self-assembly of a model tetrapod molecule with reduced symmetry. To that end, a rigid functional unit comprising a few interconnected segments arranged in different tetrapod shapes was used and its self-assembly on a triangular lattice representing a (111) crystal surface was simulated. The results of our calculations show strong dependence of the structure formation on the molecular symmetry, in particular on the (pro)chiral nature of the building block. The simulations predicted the formation of unusual ordered racemic networks with unique aperiodic spatial distribution of the surface enantiomers. Molecular symmetry was also found to have significant influence on the enantiopure self-assembly which resulted in the Kagome and brickwall networks and other less ordered extended superstructures with parallelogram pores. The theoretical findings of this contribution can be relevant to designing and on-surface synthesis of molecular superstructures with predefined geometries and functions. In particular, the predicted molecular architectures can stimulate experimental efforts to fabricate and explore new nanostructures, for example graphitic, having the composition and geometry proposed in our study.
Self-assembly of functional molecules on solid substrates has recently attracted special attention as a versatile method for the fabrication of low dimensional nanostructures with tailorable properties. In this contribution, using theoretical modeling, we demonstrate how the architecture of 2D molecular assemblies can be predicted based on the individual properties of elementary building blocks at play. To that end a model star-shaped tetratopic molecule is used and its self-assembly on a (111) surface is simulated using the lattice Monte Carlo method. Several test cases are studied in which the molecule bears terminal arm centers providing interactions with differently encoded directionality. Our theoretical results show that manipulation of the interaction directions can be an effective way to direct the self-assembly towards extended periodic superstructures (2D crystals) as well as to create assemblies characterized by a lower degree of order, including glassy overlayers and quasi one-dimensional molecular connections. The obtained structures are described and classified with respect to their main geometric parameters. A small library of the tetratopic molecules and the corresponding superstructures is provided to categorize the structure-property relationship in the modeled systems. The results of our simulations can be helpful to 2D crystal engineering and surface-confined polymerization techniques as they give hints on how to functionalize tetrapod organic building blocks which would be able to create superstructures with predefined spatial organization and range of order.
Monte Carlo simulations were used to decipher the individual role of tripod molecular conformers in the surface-confined metal-organic self-assembly. Our calculations revealed the extent of structural heterogeneity introduced by the different conformers.
Self-similar fractal structures are of fundamental importance in science, mathematics, and aesthetics. A series of molecular defect-free Sierpinski triangle fractals have been constructed on surfaces recently. However, the highest order of the fractals is only 4 because of the limitation of kinetic growth. Here complete fifth-order Sierpinski triangles with a lateral length of 0.05 µm were successfully prepared in ultrahigh vacuum by a combination of templating and coassembly methods. Fe atoms, 4,4â³-dicyano-1,1':3',1â³-terphenyl, and 1,3-bis(4-pyridyl)benzene molecules were used to build fractals on the reconstructed Au(100)-(hex) surface. The new strategy may be applied to construct various Sierpinski triangles of higher orders.
The self-assembly behavior of a V-shaped bispyridine, 1,3-bi(4-pyridyl)benzene (BPyB), was studied by scanning tunneling microscopy on the (111) surfaces of Cu, Ag, and Au. BPyB molecules coordinately bonded with active Cu adatoms on Cu(111) in the form of complete polygonal rings at low coverages. On Ag(111), BPyB molecules aggregated into two-dimensional islands by relatively weak intermolecular hydrogen bonds. The coexistence of hydrogen bonds and coordination interaction was observed on the BPyB-covered Au(111) substrate. Density functional theory calculations of the metal-molecule binding energy and Monte Carlo simulations were performed to help understand the forming mechanism of molecular superstructures on the surfaces. In particular, the comprehensive orbital composition analysis interprets the observed metal-organic complexes and reveals the importance of relativistic effects for the extraordinary activity of gold adatoms. The relativistic effects cause the energy stability of the Au 6s atomic orbital and decrease the energy separation between the Au 6s and 5d orbitals. The enhanced sd hybridization strengthens the N-Au-N bond in BPyB-Au-BPyB complexes.
Self-assembly of 1,3,5-tris(4-mercaptophenyl)benzene (TMB), a 3-fold symmetric, thiol-functionalized aromatic molecule, was studied on Au(111) with the aim of realizing extended Au-thiolate-linked molecular architectures. The focus lay on resolving thermally activated structural and chemical changes by a combination of microscopy and spectroscopy. Thus, scanning tunneling microscopy (STM) provided submolecularly resolved structural information, while the chemical state of sulfur was assessed by X-ray photoelectron spectroscopy (XPS). Directly after room-temperature deposition, only less well ordered structures were observed. Mild annealing promoted the first structural transition into ordered molecular chains, partly organized in homochiral molecular braids. Further annealing led to self-similar Sierpinski triangles, while annealing at even higher temperatures again resulted in mostly disordered structures. Both the irregular aggregates observed at room temperature and the chains were identified as metal-organic assemblies, whereby two out of the three intermolecular binding motifs are energetically equivalent according to density functional theory (DFT) simulations. The emergence of Sierpinski triangles is driven by a chemical transformation, i.e., the conversion of coordinative Au-thiolate to covalent thioether linkages, and can be further understood by Monte Carlo simulations. The great structural variance of TMB on Au(111) can on one hand be explained by the energetic equivalence of two binding motifs. On the other hand, the unexpected chemical transition even enhances the structural variance and results in thiol-derived covalent molecular architectures.
Two-dimensional polymers are of great interest for many potential applications in nanotechnology. The preparation of crystalline 2D polymers with a tunable band gap is critical for their applications in nano-electronics and optoelectronics. In this work, we try to tune the band gap of 2D imine polymers by expanding the conjugation of the backbone of aromatic diamines both laterally and longitudinally. STM characterization reveals that the regularity of the 2D polymers can be affected by the existence of lateral bulky groups. Density functional theory (DFT) simulations discovered a significant narrowing of the band gap of imine 2D polymers upon the expansion of the conjugation of the monomer backbone, which has been confirmed experimentally by UV absorption measurements. Monte Carlo simulations help us to gain further insight into the controlling factors of the formation of regular 2D polymers, which demonstrated that based on the all rigid assumption, the coexistence of different conformations of the imine moiety has a significant effect on the regularity of the imine 2D polymers.
Recent studies demonstrate that simple functional molecules, which usually form two-dimensional (2D) crystal structures when adsorbed on solid substrates, are also able to self-assemble into ordered openwork fractal aggregates. To direct and control the growth of such fractal supramolecules, it is necessary to explore the conditions under which both fractal and crystalline patterns develop and coexist. In this contribution, we study the coexistence of Sierpinski triangle (ST) fractals and 2D molecular crystals that were formed by 4,4â³-dihydroxy-1,1':3',1â³-terphenyl molecules on Au(111) in ultrahigh vacuum. Growth competition between the STs and 2D crystals was realized by tuning substrate and molecular surface coverage and changing the functional groups of the molecular building block. Density functional theory calculations and Monte Carlo simulations are used to characterize the process. Both experimental and theoretical results demonstrate the possibility of steering the surface self-assembly to generate fractal and nonfractal structures made up of the same molecular building block.
Patterning of solid surfaces with functional organic molecules has been a convenient route to fabricate two-dimensional materials with programmed architecture and activities. One example is the chiral nanoporous networks that can be created via controlled self-assembly of star-shaped molecules under 2D confinement. In this contribution we use computer modeling to predict the formation of molecular networks in adsorbed overlayers comprising cruciform molecular building blocks equipped with discrete interaction centers. To that end, we employ the Monte Carlo simulation method combined with a coarse-grained representation of the adsorbed molecules which are treated as collections of interconnected segments. The interaction centers within the molecules are represented by active segments whose number and distribution are adjusted. Our particular focus is on those distributions that produce prochiral molecules able to occur in adsorbed configurations being mirror images of each other (surface enantiomers). We demonstrate that, depending on size, aspect ratio, and intramolecular distribution of active sites, the surface enantiomers can co-crystallize or segregate into extended homochiral domains with largely diversified nanosized cavities. The insights from our theoretical studies can be helpful in designing 2D chiral porous networks with potential applications in enantioselective adsorption and asymmetric heterogeneous catalysis.
In this work we have analyzed the influence of various factors on the transverse relaxation times T2 of water protons in suspension of magnetic nanoparticles. For that purpose we developed a full molecular dynamics force field which includes the effects of dispersion interactions between magnetic nanoparticles and water molecules, electrostatic interactions between charged nanoparticles and magnetic dipole-dipole and dipole-external field interactions. We also accounted for the magnetization reversal within the nanoparticles body frames due to finite magnetic anisotropy barriers. The force field together with the Langevin dynamics imposed on water molecules and the nanoparticles allowed us to monitor the dephasing of water protons in real time. Thus, we were able to determine the T2 relaxation times including the effects of the adsorption of water on the nanoparticles' surfaces, thermal fluctuations of the orientation of nanoparticles' magnetizations as well as the effects of the core-shell architecture of nanoparticles and their agglomeration into clusters. We found that there exists an optimal cluster size for which T2 is minimized and that the retardation of water molecules motion, due to adsorption on the nanoparticles surfaces, has some effect in the measured T2 times. The typical strengths of the external magnetic fields in MRI are enough to keep the magnetizations fixed along the field direction, however, in the case of low magnetic fields, we observed significant enhancement of T2 due to thermal fluctuations of the orientations of magnetizations.
On-surface Ullmann coupling is a versatile and appropriate approach for the bottom-up fabrication of covalent organic nanostructures. In two-dimensional networks, however, the kinetically controlled and irreversible coupling leads to high defect densities and a lack of long-range order. To derive general guidelines for optimizing reaction parameters, the structural quality of 2D porous covalent networks was evaluated for different preparation protocols. For this purpose, polymerization of an iodine- and bromine-functionalized precursor was studied on Au(111) by scanning tunneling microscopy under ultrahigh vacuum conditions. By taking advantage of the vastly different temperature thresholds for C-Br and C-I cleavage, two different polymerization routes were compared - hierarchical and direct polymerization. The structural quality of the covalent networks was evaluated for different reaction parameters, such as surface temperatures, heating rates, and deposition rates by statistical analysis of STM data. Experimental results are compared to Monte Carlo simulations.
The formation of 2D surface-confined supramolecular porous networks is scientifically and technologically appealing, notably for hosting guest species and confinement phenomena. In this study, we report a scanning tunneling microscopy (STM) study of the self-assembly of a tripod molecule specifically equipped with pyridyl functional groups to steer a simultaneous expression of lateral pyridyl-pyridyl interactions and Cu-pyridyl coordination bonds. The assembly protocols yield a new class of porous open assemblies, the formation of which is driven by multiple interactions. The tripod forms a purely porous organic network on Ag(111), phase α, in which the presence of the pyridyl groups is crucial for porosity, as confirmed by molecular dynamics and Monte Carlo simulations. Additional deposition of Cu dramatically alters this scenario. For submonolayer coverage, three different porous phases coexist (i.e., ß, γ, and δ). Phases ß and γ are chiral and exhibit a simultaneous expression of lateral pyridyl-pyridyl interactions and twofold Cu-pyridyl linkages, whereas phase δ is just stabilized by twofold Cu-pyridyl bonds. An increase in the lateral molecular coverage results in a rise in molecular pressure, which leads to the formation of a new porous phase (ε), only coexisting with phase α and stabilized by a simultaneous expression of lateral pyridyl-pyridyl interactions and threefold Cu-pyridyl bonds. Our results will open new avenues to create complex porous networks on surfaces by exploiting components specifically designed for molecular recognition through multiple interactions.
Macrocyclic Compounds/chemistry , Metals/chemistry , Organometallic Compounds/chemistry , Pyridines/chemistry , Copper/chemistry , Hydrogen Bonding , Microscopy, Scanning Tunneling , Models, Molecular , Nanostructures/chemistry , Porosity
We report a joint computational and experimental study on the concentration-dependent self-assembly of a flat C3-symmetric molecule at surfaces. As a model system we have chosen a rigid molecular module, 1,3,5-tris(pyridine-4-ylethynyl)benzene, which can undergo self-association via hydrogen bonding (H-bonding) to form ordered 2D nanostructures. In particular, the lattice Monte Carlo method, combined with density functional calculations, was employed to explore the spontaneous supramolecular organization of this tripod-shaped molecule under surface confinement. We analyzed the stability of different weak H-bonded patterns and the influence of the concentration of the starting molecule on the 2D supramolecular packing. We found that ordered, densely packed monolayers and 2D porous networks are obtained at high and low concentrations, respectively. A concentration-dependent scanning tunneling microscopy investigation of the molecular self-assembly at a graphite-solution interface revealed supramolecular motifs, which are in perfect agreement with those obtained by simulations. Therefore, our computational approach represents a step forward toward the deterministic prediction of molecular self-assembly at surfaces and interfaces.
Benzene Derivatives/chemical synthesis , Nanostructures/chemistry , Pyridines/chemical synthesis , Benzene Derivatives/chemistry , Hydrogen Bonding , Macromolecular Substances/chemical synthesis , Macromolecular Substances/chemistry , Models, Molecular , Molecular Structure , Pyridines/chemistry , Surface Properties
