Predicting supramolecular self-assembly on reconstructed metal surfaces

Stable Au(111) Hexagonal Reconstruction Induced by Perchlorinated Nanographene Molecules

Surface reconstructions play a crucial role in surface science because of their influence on the adsorption and arrangement of molecules or nanoparticles. On the Au(111) surface, the herringbone reconstruction presents favorable anchoring at the elbow sites, where the highest reactivity is found. In this work, we deposited large organic perchlorinated molecules on a Au(111) surface via high-vacuum electrospray deposition. With noncontact atomic force microscopy measurements at room temperature, we studied the molecular structures formed on the surface before and after annealing at different temperatures. We found that a supramolecular layer is formed and that a hexagonal reconstruction of the Au(111) surface is induced. After high-temperature annealing, the molecules are removed, but the hexagonal Au(111) surface reconstruction is preserved. With the hexagonal Au(111) surface reconstruction, a periodic lattice of anchoring sites is formed.

3D Directional Assembly of Liquid Crystal Molecules

The precise construction of hierarchically long-range ordered structures using molecules as fundamental building blocks can fully harness their anisotropy and potential. However, the 3D, high-precision, and single-step directional assembly of molecules is a long-pending challenge. Here, a 3D directional molecular assembly strategy via femtosecond laser direct writing (FsLDW) is proposed and the feasibility of this approach using liquid crystal (LC) molecules as an illustrative example is demonstrated. The physical mechanism for femtosecond (fs) laser-induced assembly of LC molecules is investigated, and precise 3D arbitrary assembly of LC molecules is achieved by defining the discretized laser scanning pathway. Additionally, an LC-based Fresnel zone plate array with polarization selection and colorization imaging functions is fabricated to further illustrate the potential of this method. This study not only introduces a 3D high-resolution alignment method for LC-based functional devices but also establishes a universal protocol for the precise 3D directional assembly of anisotropic molecules.

Interfacial Charge Transfer Influences Thin-Film Polymorphism

The structure and chemical composition are the key parameters influencing the properties of organic thin films deposited on inorganic substrates. Such films often display structures that substantially differ from the bulk, and the substrate has a relevant influence on their polymorphism. In this work, we illuminate the role of the substrate by studying its influence on para-benzoquinone on two different substrates, Ag(111) and graphene. We employ a combination of first-principles calculations and machine learning to identify the energetically most favorable structures on both substrates and study their electronic properties. Our results indicate that for the first layer, similar structures are favorable for both substrates. For the second layer, we find two significantly different structures. Interestingly, graphene favors the one with less, while Ag favors the one with more electronic coupling. We explain this switch in stability as an effect of the different charge transfer on the two substrates.

Self-assembly and photoinduced fabrication of conductive nanographene wires on boron nitride

Manufacturing molecule-based functional elements directly at device interfaces is a frontier in bottom-up materials engineering. A longstanding challenge in the field is the covalent stabilization of pre-assembled molecular architectures to afford nanodevice components. Here, we employ the controlled supramolecular self-assembly of anthracene derivatives on a hexagonal boron nitride sheet, to generate nanographene wires through photo-crosslinking and thermal annealing. Specifically, we demonstrate µm-long nanowires with an average width of 200 nm, electrical conductivities of 10⁶S m⁻¹ and breakdown current densities of 10¹¹A m⁻². Joint experiments and simulations reveal that hierarchical self-assembly promotes their formation and functional properties. Our approach demonstrates the feasibility of combined bottom-up supramolecular templating and top-down manufacturing protocols for graphene nanomaterials and interconnects, towards integrated carbon nanodevices.

The bottom-up fabrication of structures with robust performance in the nm-to-μm scale usable for integrated carbon nanodevices is challenging. Here the authors report micrometer-long, highly conducting nanographene wires following self-assembly, photo-crosslinking and thermal annealing of anthracene derivatives on hexagonal boron nitride sheets.

Unexpected Self-Assembly Pathway to a Pd(II) Coordination Square-Based Pyramid and Its Preferential Formation beyond the Boltzmann Distribution

Experimental and theoretical investigations of the self-assembly process of a Pd(II) coordination M₆L₄ square-based pyramid (SP) were conducted. It was found that the probable self-assembly pathway, in which the dimerization of M₂L₂ with two M leads to SP, expected from the connectivity of the building blocks is not a major self-assembly pathway to the M₆L₄ SP. Whether the M₆L₄ SP is assembled or M₂L₂ is trapped is determined by an inter- or intramolecular reaction in a chain-like M₂L₂X, where X is a leaving ligand. The kinetically trapped state where the M₆L₄ SP is produced from M₂L₂ beyond the Boltzmann distribution was realized by a concentration-induced process and was kept for at least 2 months at 298 K.

From high quality packing to disordered nucleation or phase separation in donor/acceptor interfaces: ClAlPc-C60 on Au(111)

The dramatic consequences that the orientation adopted by the molecular dipoles, in diverse arrays of chloroaluminum phthalocyanine (ClAlPc) on Au(111), have on the ulterior adsorption and growth of C60 are explored by means of an all scanning probe microscopy approach. The unidirectional downwards organization of the molecular dipoles at the first layer reduces charge transfer from the metal to C60. Imbalance between attractive and repulsive interactions of the fullerenes are crucial for their ordered supramolecular aggregation. The effect at the basis of such self-assembling seems to be released by the all upwards dipole orientation adopted on the ClAlPc second layer. The low electronic corrugation of the bilayer results in a higher mobility of the fullerenes which for similar coverages diffuse large distances to reach uncovered first layer regions. Density functional theory calculations corroborate the experimental observations indicating the relevance of charge transfer, potential energy surface corrugation, C60 on-surface diffusion barriers and screening. The structure of the co-adsorbed C60 and ClAlPc layers strongly depends on the deposition sequence. Phase-separation, where each molecule adopts the single-component assembly, occurs if C60 is deposited first. The present results contribute to understanding the influence of the dipolar nature of molecular layers on the electronic and structure of donor/acceptor heterojunctions, which is crucial for device design via engineering the energy level alignment at organic-organic and organic-metal interfaces.

First-principles calculations of hybrid inorganic-organic interfaces: from state-of-the-art to best practice

The computational characterization of inorganic-organic hybrid interfaces is arguably one of the technically most challenging applications of density functional theory. Due to the fundamentally different electronic properties of the inorganic and the organic components of a hybrid interface, the proper choice of the electronic structure method, of the algorithms to solve these methods, and of the parameters that enter these algorithms is highly non-trivial. In fact, computational choices that work well for one of the components often perform poorly for the other. As a consequence, default settings for one materials class are typically inadequate for the hybrid system, which makes calculations employing such settings inefficient and sometimes even prone to erroneous results. To address this issue, we discuss how to choose appropriate atomistic representations for the system under investigation, we highlight the role of the exchange-correlation functional and the van der Waals correction employed in the calculation and we provide tips and tricks how to efficiently converge the self-consistent field cycle and to obtain accurate geometries. We particularly focus on potentially unexpected pitfalls and the errors they incur. As a summary, we provide a list of best practice rules for interface simulations that should especially serve as a useful starting point for less experienced users and newcomers to the field.

Exploring the configuration spaces of surface materials using time-dependent diffraction patterns and unsupervised learning

Computational methods for exploring the atomic configuration spaces of surface materials will lead to breakthroughs in nanotechnology and beyond. In order to develop such methods, especially ones utilizing machine learning approaches, descriptors which encode the structural features of the candidate configurations are required. In this paper, we propose the use of time-dependent electron diffraction simulations to create descriptors for the configurations of surface materials. Our proposal utilizes the fact that the sub-femtosecond time-dependence of electron diffraction patterns are highly sensitive to the arrangement of atoms in the surface region of the material, allowing one to distinguish configurations which possess identical symmetry but differ in the locations of the atoms in the unit cell. We demonstrate the effectiveness of this approach by considering the simple cases of copper(111) and an organic self-assembled monolayer system, and use it to search for metastable configurations of these materials.

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.

Adsorption of Milk Proteins (β-Casein and β-Lactoglobulin) and BSA onto Hydrophobic Surfaces

Here, we study films of proteins over planar surfaces and protein-coated microspheres obtained from the adsorption of three different proteins ( β -casein, β -lactoglobulin and bovine serum albumin (BSA)). The investigation of protein films in planar surfaces is performed by combining quartz crystal microbalance (QCM) and atomic force microscopy (AFM) measurements with all-atomic molecular dynamics (MD) simulations. We found that BSA and β -lactoglobulin form compact monolayers, almost without interstices between the proteins. However, β -casein adsorbs forming multilayers. The study of the electrokinetic mobility of protein-coated latex microspheres shows substantial condensation of ions from the buffer over the complexes, as predicted from ion condensation theories. The electrokinetic behavior of the latex-protein complexes is dominated by the charge of the proteins and the phenomenon of ion condensation, whereas the charge of the latex colloids plays only a minor role.

Structure Prediction for Surface-Induced Phases of Organic Monolayers: Overcoming the Combinatorial Bottleneck

Structure determination and prediction pose a major challenge to computational material science, demanding efficient global structure search techniques tailored to identify promising and relevant candidates. A major bottleneck is the fact that due to the many combinatorial possibilities, there are too many possible geometries to be sampled exhaustively. Here, an innovative computational approach to overcome this problem is presented that explores the potential energy landscape of commensurate organic/inorganic interfaces where the orientation and conformation of the molecules in the tightly packed layer is close to a favorable geometry adopted by isolated molecules on the surface. It is specifically designed to sample the energetically lowest lying structures, including the thermodynamic minimum, in order to survey the particularly rich and intricate polymorphism in such systems. The approach combines a systematic discretization of the configuration space, which leads to a huge reduction of the combinatorial possibilities with an efficient exploration of the potential energy surface inspired by the Basin-Hopping method. Interfacing the algorithm with first-principles calculations, the power and efficiency of this approach is demonstrated for the example of the organic molecule TCNE (tetracyanoethylene) on Au(111). For the pristine metal surface, the global minimum structure is found to be at variance with the geometry found by scanning tunneling microscopy. Rather, our results suggest the presence of surface adatoms or vacancies that are not imaged in the experiment.

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.

Surface Dipole Control of Liquid Crystal Alignment

Detailed understanding and control of the intermolecular forces that govern molecular assembly are necessary to engineer structure and function at the nanoscale. Liquid crystal (LC) assembly is exceptionally sensitive to surface properties, capable of transducing nanoscale intermolecular interactions into a macroscopic optical readout. Self-assembled monolayers (SAMs) modify surface interactions and are known to influence LC alignment. Here, we exploit the different dipole magnitudes and orientations of carboranethiol and -dithiol positional isomers to deconvolve the influence of SAM-LC dipolar coupling from variations in molecular geometry, tilt, and order. Director orientations and anchoring energies are measured for LC cells employing various carboranethiol and -dithiol isomer alignment layers. The normal component of the molecular dipole in the SAM, toward or away from the underlying substrate, was found to determine the in-plane LC director orientation relative to the anisotropy axis of the surface. By using LC alignment as a probe of interaction strength, we elucidate the role of dipolar coupling of molecular monolayers to their environment in determining molecular orientations. We apply this understanding to advance the engineering of molecular interactions at the nanoscale.

Observation and modeling of conformational molecular structures driving the self-assembly of tri-adamantyl benzene on Ag(111)

A STM image of the hexagonal network of tri-adamantyl benzene molecules on Ag(111).

Theoretical Modeling of Surface Confined Chiral Nanoporous Networks: Cruciform Molecules as Versatile Building Blocks

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.