Atomistic Simulations of 2D Bicomponent Self-Assembly: From Molecular Recognition to Self-Healing

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.

Low-power microwaves: a cell-compatible physical treatment to enhance the mechanical properties of self-assembling peptides

Biomaterials designed for tissue engineering applications should, among other requirements, mimic the native extracellular matrix (ECM) of the tissues to be regenerated, both in terms of biomimetic and mechanical properties. Ideally, the scaffold stiffness and stress resistance should be tuned for each specific implantation therapy. Self-assembling peptides (SAPs) are promising synthetic bionanomaterials prone to easy multi-functionalization, bestowing biomimetic properties. However, they usually yield soft and fragile hydrogels unsuited for the regeneration of medium-to-hard tissues. For this purpose, chemical cross-linking of SAPs is an option, but it often requires a moderately toxic and expensive chemical compound and/or the presence of specific residues/reactive sites, posing issues for its feasibility and translational potential. In this work, we introduced, characterized by rheology, atomic force microscopy (AFM), Thioflavin-T assay (ThT), and Fourier transform infrared (FT-IR) tests, and optimized (by tuning the power, temperature and treatment time) a novel fast, green and affordable methodology using mild microwave (MW) irradiation to increase the mechanical properties of diverse classes of SAPs. Low-power MWs increase stiffness, resilience, and β-structuration, while high-power MW treatments partially denature the tested SAPs. Our pure-physical methodology does not alter the SAP biomimetic properties (verified via in vitro tests of viability and differentiation of human neural stem cells), is compatible with already seeded cells, and is also synergic with genipin-based cross-linking of SAPs; therefore, it may become the next standard for SAP preparation in tissue engineering applications at hand of all research labs and in clinics.

Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net.

Co-assembly Behaviors of Flavonol Derivatives Induced by a Pyridine Derivative on HOPG via Hydrogen Bonding and Van der Waals Forces

In this paper, two new flavonol derivatives, 2-(4-(dodecyloxy)phenyl)-3-hydroxyflavone (DHF) and 2-(3,5-bis(dodecyloxy)phenyl)-3-hydroxyflavone (BDHF), were synthesized to investigate the respective self-assembly behaviors at the liquid/solid interface by scanning tunneling microscopy. In addition, a linear pyridine derivative with acetylene groups called BisPy was added to regulate the assembly of DHF and BDHF, individually. However, only BDHF molecules successfully co-assembled into grid structures with BisPy molecules. Furthermore, the assembly and co-assembly behavior mechanism of flavonol derivatives and BisPy molecules were further studied by density functional theory calculations. This work will lay a foundation for investigating the self-assembly of flavonol derivatives and the co-assembly regulated by pyridine derivatives at the liquid-solid interface.

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.

Bicomponent Coassembled Hydrogel as a Template for Selective Enzymatic Generation of DOPA

In living organisms, tyrosinase selectively produces l-DOPA from l-tyrosine. Here, a bicomponent hydrogel is used as a template for tyrosinase-catalyzed selective generation of l-DOPA from tyrosine. An amphiphilic molecule 1,5-diaminonaphthalene (DAN) coassembles with 1,3,5-benzenetricarboxylic acid (BTC) to form a self-supporting hydrogel. After alteration of complementary acids, DAN does not coassemble to form a hydrogel. The coassembly mechanism is investigated using spectroscopic techniques. The transmission electron microscopy and scanning electron microscopy images reveal the morphology details. The l-DOPA is kept from being oxidized when the hydrogel is used as a template. The enzymatically synthesized l-DOPA can also be separated from the mixture by easy tuning of the bicomponent coassembly.

Neuroevolutionary Learning of Particles and Protocols for Self-Assembly

Within simulations of molecules deposited on a surface we show that neuroevolutionary learning can design particles and time-dependent protocols to promote self-assembly, without input from physical concepts such as thermal equilibrium or mechanical stability and without prior knowledge of candidate or competing structures. The learning algorithm is capable of both directed and exploratory design: it can assemble a material with a user-defined property, or search for novelty in the space of specified order parameters. In the latter mode it explores the space of what can be made, rather than the space of structures that are low in energy but not necessarily kinetically accessible.

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.

Two-dimensional co-crystallization of two carboxylic acid derivatives having dissimilar symmetries at the liquid/solid interface

By the co-assembly of two carboxylic acids with distinct symmetries and different numbers of carboxyl groups, we obtained two novel cocrystal structures at the n-octanoic acid/HOPG interface, one of which was sustained by unoptimized R22(8) hydrogen bonding. Benefiting from the bias-sensitivity of the BTB (1,3,5-tris(4-carboxyphenyl)benzene) molecule, a structure transition between the cocrystal network and a denser BTB lamella is achieved.

Simulations of the 2D self-assembly of tripod-shaped building blocks

We introduce a molecular dynamics (MD) coarse-grained model for the description of tripod building blocks. This model has been used by us already for linear, V-shape, and tetratopic molecules. We wanted to further extend its possibilities to trifunctional molecules to prove its versatility. For the chosen systems we have also compared the MD results with Monte Carlo results on a triangular lattice. We have shown that the constraints present in the latter method can enforce the formation of completely different structures, not reproducible with off-lattice simulations. In addition to that, we have characterized the obtained structures regarding various parameters such as theoretical diffraction pattern and average association number.

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.

Controlling a Chemical Coupling Reaction on a Surface: Tools and Strategies for On-Surface Synthesis

On-surface synthesis is appearing as an extremely promising research field aimed at creating new organic materials. A large number of chemical reactions have been successfully demonstrated to take place directly on surfaces through unusual reaction mechanisms. In some cases the reaction conditions can be properly tuned to steer the formation of the reaction products. It is thus possible to control the initiation step of the reaction and its degree of advancement (the kinetics, the reaction yield); the nature of the reaction products (selectivity control, particularly in the case of competing processes); as well as the structure, position, and orientation of the covalent compounds, or the quality of the as-formed networks in terms of order and extension. The aim of our review is thus to provide an extensive description of all tools and strategies reported to date and to put them into perspective. We specifically define the different approaches available and group them into a few general categories. In the last part, we demonstrate the effective maturation of the on-surface synthesis field by reporting systems that are getting closer to application-relevant levels thanks to the use of advanced control strategies.

On-surface self-assembly of tetratopic molecular building blocks

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.

Concentration-dependent supramolecular patterns of C3 and C2 symmetric molecules at the solid/liquid interface

Here we report on a scanning tunnelling microscopy (STM) investigation on the self-assembly of C₃- and C₂-symmetric molecules at the solution/graphite interface. 1,3,5-tris((E)-2-(pyridin-4-yl)vinyl)benzene and 1,1,2,2-tetrakis(4-(pyridin-4-yl)phenyl)ethane are used as model systems. These molecules displayed a concentration dependent self-assembly behaviour on graphite, resulting in highly ordered supramolecular structures, which are stabilized jointly by van der Waals substrate-adsorbate interactions and in-plane intermolecular H-bonding. Denser packing is obtained when applying a relatively high concentration solution to the basal plane of the surface whereas a less dense porous network is observed upon lowering the concentration. We show that the molecular conformation does not influence the stability of the self-assembly and a twisted molecule can pack into dense and porous architectures under the concentration effect.

Electrostatically Driven Guest Binding in a Self-Assembled Porous Network at the Liquid/Solid Interface

We present here the construction of a self-assembled two-dimensional (2D) porous monolayer bearing a highly polar 2D space to study guest co-adsorption through electrostatic interactions at the liquid/solid interface. For this purpose, a dehydrobenzo[12]annulene (DBA) derivative, DBA-TeEG, having tetraethylene glycol (TeEG) groups at the end of the three alternating alkoxy chains connected by p-phenylene linkers was synthesized. As a reference host molecule, DBA-C10, having nonpolar C₁₀ alkyl chains at three alternating terminals, was employed. As guest molecules, hexagonal phenylene-ethynylene macrocycles (PEMs) attached by triethylene glycol (TEG) ester and hexyl ester groups, PEM-TEG and PEM-C6, respectively, at each vertex of the macrocyclic periphery were used. Scanning tunneling microscopy observations at the 1,2,4-trichlorobenzene/highly oriented pyrolytic graphite interface revealed that PEM-TEG was immobilized in the pores formed by DBA-TeEG at higher probability because of electrostatic interactions such as dipole-dipole and hydrogen bonding interactions between oligoether units of the host and guest, in comparison to PEM-C6 with nonpolar groups. These observations are discussed based on molecular mechanics simulations to investigate the role of the polar functional groups. When a nonpolar host matrix formed by DBA-C10 was used, however, only phase separation and preferential adsorption were observed; virtually no host-guest complexation was discernible. This is ascribed to the strong affinity between the guest molecules which form by themselves densely packed van der Waals networks on the surface.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.

Harnessing complexity in molecular self-assembly using computer simulations

In molecular self-assembly, hundreds of thousands of freely-diffusing molecules associate to form ordered and functional architectures in the absence of an actuator. This intriguing phenomenon plays a critical role in biology and has become a powerful tool for the fabrication of advanced nanomaterials. Due to the limited spatial and temporal resolutions of current experimental techniques, computer simulations offer a complementary strategy to explore self-assembly with atomic resolution. Here, we review recent computational studies focusing on both thermodynamic and kinetic aspects. As we shall see, thermodynamic approaches based on modeling and statistical mechanics offer initial guidelines to design nanostructures with modest computational effort. Computationally more intensive analyses based on molecular dynamics simulations and kinetic network models (KNMs) reach beyond it, opening the door to the rational design of self-assembly pathways. Current limitations of these methodologies are discussed. We anticipate that the synergistic use of thermodynamic and kinetic analyses based on computer simulations will provide an important contribution to the de novo design of self-assembly.

Enantiomer surface chemistry: conglomerate versus racemate formation on surfaces

Research on surface chirality is motivated by the need to develop functional chiral surfaces for enantiospecific applications. While molecular chirality in 3D has been the subject of study for almost two centuries, many aspects of 2D chiral surface chemistry have yet to be addressed. In 3D, racemic mixtures of chiral molecules tend to aggregate into racemate (molecularly heterochiral) crystals much more frequently than conglomerate (molecularly homochiral) crystals. Whether chiral adsorbates on surfaces preferentially aggregate into heterochiral rather than homochiral domains (2D crystals or clusters) is not known. In this review, we have made the first attempt to answer the following question based on available data: in 2D racemic mixtures adsorbed on surfaces, is there a clear preference for homochiral or heterochiral aggregation? The current hypothesis is that homochiral packing is preferred on surfaces; in contrast to 3D where heterochiral packing is more common. In this review, we present a simple hierarchical scheme to categorize the chirality of adsorbate-surface systems. We then review the body of work using scanning tunneling microscopy predominantly to study aggregation of racemic adsorbates. Our analysis of the existing literature suggests that there is no clear evidence of any preference for either homochiral or heterochiral aggregation at the molecular level by chiral and prochiral adsorbates on surfaces.

Exploitation of the Large-Area Basal Plane of MoS2 and Preparation of Bifunctional Catalysts through On-Surface Self-Assembly

The development of nonprecious electrochemical catalysts for water splitting is a key step to achieve a sustainable energy supply for the future. Molybdenum disulfide (MoS2) has been extensively studied as a promising low-cost catalyst for hydrogen evolution reaction (HER), whereas HER is only catalyzed at the edge for pristine MoS2, leaving a large area of basal plane useless. Herein, on-surface self-assembly is demonstrated to be an effective, facile, and damage-free method to take full advantage of the large ratio surface of MoS2 for HER by using multiscale simulations. It is found that as supplement of edge sites of MoS2, on-MoS2 M(abt)2 (M = Ni, Co; abt = 2-aminobenzenethiolate) owns high HER activity, and the self-assembled M(abt)2 monolayers on MoS2 can be obtained through a simple liquid-deposition method. More importantly, on-surface self-assembly provides potential application for overall water splitting once the self-assembled systems prove to be of both HER and oxygen evolution reaction activities, for example, on-MoS2 Co(abt)2. This work opens up a new and promising avenue (on-surface self-assembly) toward the full exploitation of the basal plane of MoS2 for HER and the preparation of bifunctional catalysts for overall water splitting.

Kinetics-Controlled Amphiphile Self-Assembly Processes

Amphiphile self-assembly is an essential bottom-up approach of fabricating advanced functional materials. Self-assembled materials with desired structures are often obtained through thermodynamic control. Here, we demonstrate that the selection of kinetic pathways can lead to drastically different self-assembled structures, underlining the significance of kinetic control in self-assembly. By constructing kinetic network models from large-scale molecular dynamics simulations, we show that two largely similar amphiphiles, 1-[11-oxo-11-(pyren-1-ylmethoxy)-undecyl]pyridinium bromide (PYR) and 1-(11-((5a1,8a-dihydropyren-1-yl)methylamino)-11-oxoundecyl)pyridinium bromide (PYN), prefer distinct kinetic assembly pathways. While PYR prefers an incremental growth mechanism and forms a nanotube, PYN favors a hopping growth pathway leading to a vesicle. Such preference was found to originate from the subtle difference in the distributions of hydrophobic and hydrophilic groups in their chemical structures, which leads to different rates of the adhesion process among the aggregating micelles. Our results are in good agreement with experimental results, and accentuate the role of kinetics in the rational design of amphiphile self-assembly.

Porous Hydrogen-Bonded Organic Frameworks

Ordered porous solid-state architectures constructed via non-covalent supramolecular self-assembly have attracted increasing interest due to their unique advantages and potential applications. Porous metal-coordination organic frameworks (MOFs) are generated by the assembly of metal coordination centers and organic linkers. Compared to MOFs, porous hydrogen-bonded organic frameworks (HOFs) are readily purified and recovered via simple recrystallization. However, due to lacking of sufficiently ability to orientate self-aggregation of building motifs in predictable manners, rational design and preparation of porous HOFs are still challenging. Herein, we summarize recent developments about porous HOFs and attempt to gain deeper insights into the design strategies of basic building motifs.

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.

Photoresponse of supramolecular self-assembled networks on graphene-diamond interfaces

Nature employs self-assembly to fabricate the most complex molecularly precise machinery known to man. Heteromolecular, two-dimensional self-assembled networks provide a route to spatially organize different building blocks relative to each other, enabling synthetic molecularly precise fabrication. Here we demonstrate optoelectronic function in a near-to-monolayer molecular architecture approaching atomically defined spatial disposition of all components. The active layer consists of a self-assembled terrylene-based dye, forming a bicomponent supramolecular network with melamine. The assembly at the graphene-diamond interface shows an absorption maximum at 740 nm whereby the photoresponse can be measured with a gallium counter electrode. We find photocurrents of 0.5 nA and open-circuit voltages of 270 mV employing 19 mW cm⁻² irradiation intensities at 710 nm. With an ex situ calculated contact area of 9.9 × 10² μm², an incident photon to current efficiency of 0.6% at 710 nm is estimated, opening up intriguing possibilities in bottom-up optoelectronic device fabrication with molecular resolution.

Two-dimensional, self-assembled heteromolecular networks often lack functionality. Here the authors study the photoresponse of self-assembled heteromolecular networks, while controlling their positions and interfaces at an atomic level, suggesting bottom-up assembly of optoelectronics devices.

Atomically Precise Prediction of 2D Self-Assembly of Weakly Bonded Nanostructures: STM Insight into Concentration-Dependent Architectures

A joint experimental and computational study is reported on the concentration-dependant self-assembly of a flat C3 -symmetric molecule on a graphite surface. As a model system a tripodal molecule, 1,3,5-tris(pyridin-3-ylethynyl)benzene, has been chosen, which can adopt either C3h or Cs symmetry when planar, as a result of pyridyl rotation along the alkynyl spacers. Density functional theory (DFT) simulations of 2D nanopatterns with different surface coverage reveal that the molecule can generate different types of self-assembled motifs. The stability of fourteen 2D patterns and the influence of concentration are analyzed. It is found that ordered, densely packed monolayers and 2D porous networks are obtained at high and low concentrations, respectively. A concentration-dependent scanning tunneling microscopy (STM) investigation of this molecular self-assembly system at a solution/graphite interface reveals four supramolecular motifs, which are in perfect agreement with those predicted by simulations. Therefore, this DFT method represents a key step forward toward the atomically precise prediction of molecular self-assembly on surfaces and at interfaces.

Examples of Molecular Self-Assembly at Surfaces

The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that are kinetically trapped. Here we review examples of self-assembly at surfaces focusing on a physical understanding of what causes patterns seen in experiment. Some apparently disparate systems can be described in similar physical terms, indicating that simple factors - such as the geometry and energy scale of intermolecular binding - are key to understanding the self-assembly of those systems.

Synthesis of Functionalized Mono-, Bis-, and Trisethynyltriptycenes for One-Dimensional Self-Assembly on Surfaces

This paper describes the synthesis of triptycene-based building blocks that are able to interact through hydrogen bonds to form one-dimensional self-assembled motifs on surfaces. We designed 9,10-diethynyltriptycene derivatives functionalized at the ethynyl end groups by a variety of hydrogen-bonding groups for homomolecular recognition and complementary building blocks for heteromolecular recognition. We also present the synthesis of bis- and trisethynyltriptycenes with terminal alkyne functional groups available for on-surface azide-alkyne cycloaddition reaction to expand the potential of the triptycene building block.

Sulfate assimilation pathway intermediate phosphoadenosine 59-phosphosulfate acts as a signal molecule affecting production of curli fibres in Escherichia coli

The enterobacterium Escherichia coli can utilize a variety of molecules as sulfur sources, including cysteine, sulfate, thiosulfate and organosulfonates. An intermediate of the sulfate assimilation pathway, adenosine 59-phosphosulfate (APS), also acts as a signal molecule regulating the utilization of different sulfur sources. In this work, we show that inactivation of the cysH gene, leading to accumulation of phosphoadenosine 59-phosphosulfate (PAPS), also an intermediate of the sulfate assimilation pathway, results in increased surface adhesion and cell aggregation by activating the expression of the curli-encoding csgBAC operon. In contrast, curli production was unaffected by the inactivation of any other gene belonging to the sulfate assimilation pathway. Overexpression of the cysH gene downregulated csgBAC transcription, further suggesting a link between intracellular PAPS levels and curli gene expression. In addition to curli components, the Flu, OmpX and Slp proteins were also found in increased amounts in the outer membrane compartment of the cysH mutant; deletion of the corresponding genes suggested that these proteins also contribute to surface adhesion and cell surface properties in this strain. Our results indicate that, similar to APS, PAPS also acts as a signal molecule, albeit with a distinct mechanism and role: whilst APS regulates organosulfonate utilization, PAPS would couple availability of sulfur sources to remodulation of the cell surface, as part of a more global effect on cell physiology.

Emergent rhombus tilings from molecular interactions with M-fold rotational symmetry

We show that model molecules with particular rotational symmetries can self-assemble into network structures equivalent to rhombus tilings. This assembly happens in an emergent way, in the sense that molecules spontaneously select irregular fourfold local coordination from a larger set of possible local binding geometries. The existence of such networks can be rationalized by simple geometrical arguments, but the same arguments do not guarantee a network's spontaneous self-assembly. This class of structures must in certain regimes of parameter space be able to reconfigure into networks equivalent to triangular tilings.

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.

Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis

Burkholderia thailandensis, although normally avirulent for mammals, can infect macrophages in vitro and has occasionally been reported to cause pneumonia in humans. It is therefore used as a model organism for the human pathogen B. pseudomallei, to which it is closely related phylogenetically. We characterized the B. thailandensis clinical isolate CDC2721121 (BtCDC272) at the genome level and studied its response to environmental cues associated with human host colonization, namely, temperature and oxygen limitation. Effects of the different growth conditions on BtCDC272 were studied through whole genome transcription studies and analysis of proteins associated with the bacterial cell surface. We found that growth at 37°C, compared to 28°C, negatively affected cell motility and flagella production through a mechanism involving regulation of the flagellin-encoding fliC gene at the mRNA stability level. Growth in oxygen-limiting conditions, in contrast, stimulated various processes linked to virulence, such as lipopolysaccharide production and expression of genes encoding protein secretion systems. Consistent with these observations, BtCDC272 grown in oxygen limitation was more resistant to phagocytosis and strongly induced the production of inflammatory cytokines from murine macrophages. Our results suggest that, while temperature sensing is important for regulation of B. thailandensis cell motility, oxygen limitation has a deeper impact on its physiology and constitutes a crucial environmental signal for the production of virulence factors.

Nano- and microstructuration of supramolecular materials driven by H-bonded uracil·2,6-diamidopyridine complexes

In the last few decades, multiple H-bonded arrays have been shown to be versatile tools to prepare functional supramolecular materials. Supramolecular complexes formed by uracil (Ur) and 2,6-diamidopyridine (DAP) developed by Lehn are the first examples of multiple H-bonded systems governing the formation of supramolecular polymers in solution. Although a large variety of complementary multiple H-bonded complexes has been prepared, the use of the heteromolecular Ur·DAP complex still remains very promising due to its ease of preparation and its intermediate association strength that ensures a dynamical character to the self-assembly and self-organisation processes. In this feature article, we report a detailed account on the results that our group has obtained in this field by designing and engineering a novel library of shape persistent molecular modules able to transfer their geometrical information to the final supramolecular architectures through the formation of Ur·DAP complexes both at the nanoscopic and microscopic levels.

DNA and nuclear aggregates of polyamines

Polyamines (PAs) are linear polycations that are involved in many biological functions. Putrescine, spermidine and spermine are highly represented in the nucleus of eukaryotic cells and have been the subject of decades of extensive research. Nevertheless, their capability to modulate the structure and functions of DNA has not been fully elucidated. We found that polyamines self-assemble with phosphate ions in the cell nucleus and generate three forms of compounds referred to as Nuclear Aggregates of Polyamines (NAPs), which interact with genomic DNA. In an in vitro setting that mimics the nuclear environment, the assembly of PAs occurs within well-defined ratios, independent of the presence of the DNA template. Strict structural and functional analogies exist between the in vitro NAPs (ivNAPs) and their cellular homologues. Atomic force microscopy showed that ivNAPs, as theoretically predicted, have a cyclic structure, and in the presence of DNA, they form a tube-like arrangement around the double helix. Features of the interaction between ivNAPs and genomic DNA provide evidence for the decisive role of "natural" NAPs in regulating important aspects of DNA physiology, such as conformation, protection and packaging, thus suggesting a new vision of the functions that PAs accomplish in the cell nucleus.

Self-templating 2D supramolecular networks: a new avenue to reach control over a bilayer formation

One of the greatest challenges in 2D self-assembly at interfaces is the ability to grow spatially controlled supramolecular motifs in the third dimension, exploiting the surface as a template. In this manuscript a concentration-dependent study by scanning tunneling microscopy at the solid-liquid interface, corroborated by Molecular Dynamics (MD) simulations, reveals the controlled generation of mono- or bilayer self-assembled Kagomé networks based on a fully planar tetracarboxylic acid derivative. By programming the backbone of the molecular building blocks, we present a strategy to gain spatial control over the adlayer structure by conferring self-templating capacity to the 2D self-assembled network.

Supramolecular assembly/reassembly processes: molecular motors and dynamers operating at surfaces

Among the many significant advances within the field of supramolecular chemistry over the past decades, the development of the so-called "dynamers" features a direct relevance to materials science. Defined as "combinatorial dynamic polymers", dynamers are constitutional dynamic systems and materials resulting from the application of the principles of supramolecular chemistry to polymer science. Like supramolecular materials in general, dynamers are reversible dynamic multifunctional architectures, capable of modifying their constitution by exchanging, recombining, incorporating components. They may exhibit a variety of novel properties and behave as adaptive materials. In this review we focus on the design of responsive switchable monolayers, i.e. monolayers capable to undergo significant changes in their physical or chemical properties as a result of external stimuli. Scanning tunneling microscopy studies provide direct evidence with a sub-nanometre resolution, on the formation and dynamic response of these self-assembled systems featuring controlled geometries and properties.