Molecular self-assembly on two-dimensional atomic crystals: insights from molecular dynamics simulations

Stripe-Like hBN Monolayer Template for Self-Assembly and Alignment of Pentacene Molecules

Metallic surfaces with unidirectional anisotropy are often used to guide the self-assembly of organic molecules along a particular direction. Such supports thus offer an avenue for the fabrication of hybrid organic-metal interfaces with tailored morphology and precise elemental composition. Nonetheless, such control often comes at the expense of detrimental interfacial interactions that might quench the pristine properties of molecules. Here, hexagonal boron nitride grown on Ir(100) is introduced as a robust platform with several coexisting 1D stripe-like moiré superstructures that effectively guide unidirectional self-assemblies of pentacene molecules, concomitantly preserving their pristine electronic properties. In particular, highly-aligned longitudinal arrays of equally-oriented molecules are formed along two perpendicular directions, as demonstrated by comprehensive scanning tunneling microscopy and photoemission characterization performed at the local and non-local scale, respectively. The functionality of the template is demonstrated by photoemission tomography, a surface-averaging technique requiring a high degree of orientational order of the probed molecules. The successful identification of pentacene's pristine frontier orbitals underlines that the template induces excellent long-range molecular ordering via weak interactions, preventing charge transfer.

Structural Quantification of the Surface-Confined Metal-Organic Precursors Simulated with the Lattice Monte Carlo Method

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.

2D Polymer Nanonets: Controllable Constructions and Functional Applications

Two-dimensional (2D) polymer nanonets have demonstrated great potential in various application fields due to their integrated advantages of ultrafine diameter, small pore size, high porosity, excellent interconnectivity, and large specific surface area. Here, a comprehensive overview of the controlled constructions of the polymer nanonets derived from electrospinning/netting, direct electronetting, self-assembly of cellulose nanofibers, and nonsolvent-induced phase separation is provided. Then, the widely researched multifunctional applications of polymer nanonets in filtration, sensor, tissue engineering, and electricity are also given. Finally, the challenges and possible directions for further developing the polymer nanonets are also intensively highlighted. This article is protected by copyright. All rights reserved.

van der Waals Epitaxy of Organic Semiconductor Thin Films on Atomically Thin Graphene Templates for Optoelectronic Applications

ConspectusOrganic semiconductors (OSCs) offer unique advantages with respect to mechanical flexibility, low-cost processing, and tunable properties. The optical and electrical properties of devices based on OSCs can be greatly improved when an OSC is coupled with graphene in a certain manner. Our research group has focused on using graphene as a growth template for OSCs and incorporating such high-quality heterostructures into optoelectronic devices. The idea is that graphene's atomically flat surface with a uniform sp² carbon network can serve as a perfect quasi-epitaxial template for the growth of OSCs. In addition, OSC-graphene heterostructures benefit from graphene's unique characteristics, such as its high charge-carrier mobility, excellent optical transparency, and fascinating mechanical durability and flexibility.However, we have often found that OSC molecules assemble on graphene in unpredictable manners that vary from batch to batch. From observations of numerous research systems, we elucidated the mechanism underlying such poor repeatability and set out a framework to actually control the template effect of graphene on OSCs. In this Account, we not only present our scientific findings in this spectrum of areas but also convey our research scheme to the readers so that similar heterostructure complexes can be systematically studied.We began with experiments showing that the growth of OSCs on a graphene surface was driven by van der Waals interactions and is therefore sensitive to the cleanliness of the graphene surface. Nonetheless, we noted that, even on similarly clean graphene surfaces, the OSC thin film still varied with the underlying substrate. Thanks to the graphene-transfer method and in situ gating methods that we developed, we discovered that the decisive parameter for molecule-graphene interaction (and, hence, for the growth of OSCs on graphene) is the charge density in the graphene. Thus, to prepare a graphene template for high-quality graphene-OSC heterostructures, we controlled the charge density in the graphene to minimize the molecule-graphene interaction. Moreover, the possible charge transfer between OSC molecules and graphene, which induces additional molecule-graphene interactions, should also be taken into account. Eventually, we demonstrated a wide range of optoelectronic applications that benefitted from high-quality OSC-graphene heterostructures fabricated using our proof-of-concept systems.

Self-Assembly of MoS2 Monolayer Sheets by Desulfurization

Self-assembled structures of two-dimensional (2D) materials exhibit novel physical properties distinct from those of their parent materials. Herein, the critical role of desulfurization on the self-assembled structural morphologies of molybdenum disulfide (MoS₂) monolayer sheets is explored using molecular dynamics (MD) simulations. MD results show that there are differences in the atomic energetics of MoS₂ monolayer sheets with different desulfurization contents. Both free-standing and substrate-hosted MoS₂ monolayer sheets show diversity in structural morphologies, for example, flat plane structures, wrinkles, nanotubes, and folds, depending on the desulfurization contents, planar dimensions, and ratios of length to width of MoS₂ sheets. Particularly, at the critical desulfurization content, they can roll up into nanotubes, which is in good agreement with previous experimental observations. Importantly, these observed differences in the molecular structural morphologies between free-standing and substrate-hosted MoS₂ monolayer sheets can be attributed to interatomic interactions and interlayer van der Waals interactions. Furthermore, MD results have demonstrated that the surface-driven stability of MoS₂ structures can be indicated by the desulfurization contents on one surface of MoS₂ monolayer sheets, and the self-assembly of MoS₂ monolayer sheets by desulfurization can emerge to adjust their surface-driven stability. The study provides important atomic insights into tuning the self-assembling structural morphologies of 2D materials through defect engineering in the future science and engineering applications.

Designing 2D covalent networks with lattice Monte Carlo simulations: precursor self-assembly

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.

Observing the three-dimensional terephthalic acid supramolecular growth mechanism on a stearic acid buffer layer by molecular simulation methods

The terephthalic acid (TPA) supramolecular growth mechanisms on the stearic acid (STA) buffer layer, such as the phase separation and layer-by-layer (LBL) mechanisms, were considered by molecular simulations.

Surface-Confined Self-Assembly of Asymmetric Tetratopic Molecular 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.

Exploring self-organization of molecular tether molecules on a gold surface by global structure optimization

We employ nondeterministic global cluster structure optimization, based on the evolutionary algorithms paradigm, to model the self-assembly of complex molecules on a surface. As a real-life application example directly related to many recent experiments, we use this approach for the assembly of triazatriangulene "platform" molecules on the Au(111) surface. Without additional restrictions like spatial discretizations, coarse-graining or precalculated adsorption poses, and despite the proof-of-principle character of this study, we achieve satisfactory qualitative agreement with several experimental observations and can provide answers to questions that experiments on these species had left open so far. © 2019 Wiley Periodicals, Inc.

Millimeter-Sized Two-Dimensional Molecular Crystalline Semiconductors with Precisely Defined Molecular Layers via Interfacial-Interaction-Modulated Self-Assembly

The newly emerging field in organic electronics is to control the molecule-substrate interface properties at a two-dimensional (2D) limit via interfacial interactions, which paves the way for driving the molecular assembly for highly ordered 2D molecular crystalline films with precise molecular layers and large-area uniformity. Here, by exploiting molecule-substrate van der Waals (vdW) interactions, we demonstrate thermally induced self-assembly of 2D organic crystalline films exhibiting well-defined molecular layer number over a millimeter-sized area. The organic field-effect transistors (OFETs) with bilayer films show excellent electrical performance with a maximum mobility of 12.8 cm² V^-1 s^-1. Moreover, we find that the monolayer films can act as interfacial molecular templates to construct heterojunctions with well-balanced ambipolar transport behaviors. The capability of thermally induced self-assembly of 2D molecular crystalline films with controllable molecular layers and scale-up coverage opens up a way for realizing complicated electronic applications, such as lateral heterojunctions and superlattices.

Quantitative determination of a model organic/insulator/metal interface structure

By combining X-ray photoelectron spectroscopy, X-ray standing waves and scanning tunneling microscopy, we investigate the geometric and electronic structure of a prototypical organic/insulator/metal interface, namely cobalt porphine on monolayer hexagonal boron nitride (h-BN) on Cu(111). Specifically, we determine the adsorption height of the organic molecule and show that the original planar molecular conformation is preserved in contrast to the adsorption on Cu(111). In addition, we highlight the electronic decoupling provided by the h-BN spacer layer and find that the h-BN-metal separation is not significantly modified by the molecular adsorption. Finally, we find indication of a temperature dependence of the adsorption height, which might be a signature of strongly-anisotropic thermal vibrations of the weakly bonded molecules.

Dynamics of self-assembled cytosine nucleobases on graphene

Molecular self-assembly of cytosine (C _n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C _n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C _n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C _n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.

From dynamic self-assembly to networked chemical systems

Although dynamic self-assembly, DySA, is a relatively new area of research, the past decade has brought numerous demonstrations of how various types of components - on scales from (macro)molecular to macroscopic - can be arranged into ordered structures thriving in non-equilibrium, steady states. At the same time, none of these dynamic assemblies has so far proven practically relevant, prompting questions about the field's prospects and ultimate objectives. The main thesis of this Review is that formation of dynamic assemblies cannot be an end in itself - instead, we should think more ambitiously of using such assemblies as control elements (reconfigurable catalysts, nanomachines, etc.) of larger, networked systems directing sequences of chemical reactions or assembly tasks. Such networked systems would be inspired by biology but intended to operate in environments and conditions incompatible with living matter (e.g., in organic solvents, elevated temperatures, etc.). To realize this vision, we need to start considering not only the interactions mediating dynamic self-assembly of individual components, but also how components of different types could coexist and communicate within larger, multicomponent ensembles. Along these lines, the review starts with the discussion of the conceptual foundations of self-assembly in equilibrium and non-equilibrium regimes. It discusses key examples of interactions and phenomena that can provide the basis for various DySA modalities (e.g., those driven by light, magnetic fields, flows, etc.). It then focuses on the recent examples where organization of components in steady states is coupled to other processes taking place in the system (catalysis, formation of dynamic supramolecular materials, control of chirality, etc.). With these examples of functional DySA, we then look forward and consider conditions that must be fulfilled to allow components of multiple types to coexist, function, and communicate with one another within the networked DySA systems of the future. As the closing examples show, such systems are already appearing heralding new opportunities - and, to be sure, new challenges - for DySA research.

Chemical and entropic control on the molecular self-assembly process

Molecular self-assembly refers to the spontaneous assembly of molecules into larger structures. In order to exploit molecular self-assembly for the bottom-up synthesis of nanomaterials, the effects of chemical control (strength of the directionality in the intermolecular interaction) and entropic control (temperature) on the self-assembly process should be clarified. Here we present a theoretical methodology that unambiguously distinguishes the effects of chemical and entropic control on the self-assembly of molecules adsorbed to metal surfaces. While chemical control simply increases the formation probability of ordered structures, entropic control induces a variety of effects. These effects range from fine structure modulation of ordered structures, through to degrading large, amorphous structures into short, chain-shaped structures. Counterintuitively, the latter effect shows that entropic control can improve molecular ordering. By identifying appropriate levels of chemical and entropic control, our methodology can, therefore, identify strategies for optimizing the yield of desired nanostructures from the molecular self-assembly process.

Orientation-dependent energy level alignment and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on HOPG

Combining ultraviolet photoemission spectroscopy, X-ray photoemission spectroscopy, atomic force microscopy, and X-ray diffraction measurements, we performed a systematic investigation on the correlation of energy level alignment, film growth, and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on highly oriented pyrolytic graphite. The molecules lie down in the first layer and then stand up from the second layer. The ionization potential shows a sharp decrease from the lying down region to the standing up region. When C8-BTBT molecules start standing up, unconventional energy level band-bending-like shifts are observed as the film thickness increases. These shifts are ascribed to gradual decreasing of the molecular tilt angle about the substrate normal with the increasing film thickness.

Precise, Self-Limited Epitaxy of Ultrathin Organic Semiconductors and Heterojunctions Tailored by van der Waals Interactions

Precise assembly of semiconductor heterojunctions is the key to realize many optoelectronic devices. By exploiting the strong and tunable van der Waals (vdW) forces between graphene and organic small molecules, we demonstrate layer-by-layer epitaxy of ultrathin organic semiconductors and heterostructures with unprecedented precision with well-defined number of layers and self-limited characteristics. We further demonstrate organic p-n heterojunctions with molecularly flat interface, which exhibit excellent rectifying behavior and photovoltaic responses. The self-limited organic molecular beam epitaxy (SLOMBE) is generically applicable for many layered small-molecule semiconductors and may lead to advanced organic optoelectronic devices beyond bulk heterojunctions.