Direct Imaging of the Induced‐Fit Effect in Molecular Self‐Assembly

Molecular recognition is a crucial driving force for molecular self‐assembly. In many cases molecules arrange in the lowest energy configuration following a lock‐and‐key principle. When molecular flexibility comes into play, the induced‐fit effect may govern the self‐assembly. Here, the self‐assembly of dicyanovinyl‐hexathiophene (DCV6T) molecules, a prototype specie for highly efficient organic solar cells, on Au(111) by using low‐temperature scanning tunneling microscopy and atomic force microscopy is investigated. DCV6T molecules assemble on the surface forming either islands or chains. In the islands the molecules are straight—the lowest energy configuration in gas phase—and expose the dicyano moieties to form hydrogen bonds with neighbor molecules. In contrast, the structure of DCV6T molecules in the chain assemblies deviates significantly from their gas‐phase analogues. The seemingly energetically unfavorable bent geometry is enforced by hydrogen‐bonding intermolecular interactions. Density functional theory calculations of molecular dimers quantitatively demonstrate that the deformation of individual molecules optimizes the intermolecular bonding structure. The intermolecular bonding energy thus drives the chain structure formation, which is an expression of the induced‐fit effect.     

Tuning Molecular Self‐Assembly on Bulk Insulator Surfaces by Anchoring of the Organic Building Blocks

Molecular self‐assembly constitutes a versatile strategy for creating functional structures on surfaces. Tuning the subtle balance between intermolecular and molecule‐surface interactions allows structure formation to be tailored at the single‐molecule level. While metal surfaces usually exhibit interaction strengths in an energy range that favors molecular self‐assembly, dielectric surfaces having low surface energies often lack sufficient interactions with adsorbed molecules. As a consequence, application‐relevant, bulk insulating materials pose significant challenges when considering them as supporting substrates for molecular self‐assembly. Here, the current status of molecular self‐assembly on surfaces of wide‐bandgap dielectric crystals, investigated under ultrahigh vacuum conditions at room temperature, is reviewed. To address the major issues currently limiting the applicability of molecular self‐assembly principles in the case of dielectric surfaces, a systematic discussion of general strategies is provided for anchoring organic molecules to bulk insulating materials.     

Effects of crystal structures and intermolecular interactions on charge transport properties of organic semiconductors

In this study, the effects of the packing configuration and intermolecular interaction on the transport properties are investigated based on density functional theory. Molecular design from the standpoint of a quantum-chemical view is helpful to engender favorable molecular packing motifs. The transfer integral along the orientation with π–π overlap is much larger than other directions without π–π overlap, and the mobility along this orientation is higher than that along other directions. The intermolecular interaction analyses demonstrate that hydrogen bonds play a crucial role with strong electrostatic interactions in charge transfer. There will be a synergistic relationship when the π–π stacking and intermolecular interaction coexist in the same direction. It turns out that intermolecular interactions are responsible for charge transport, while π–π stacking interactions dominate donor–acceptor transport. Incorporating the understanding of the molecular packing motifs and intermolecular interactions into the design of organic semiconductors can assist in the development of novel materials.     

Engineering On‐Surface Spin Crossover: Spin‐State Switching in a Self‐Assembled Film of Vacuum‐Sublimable Functional Molecule

The realization of spin‐crossover (SCO)‐based applications requires study of the spin‐state switching characteristics of SCO complex molecules within nanostructured environments, especially on surfaces. Except for a very few cases, the SCO of a surface‐bound thin molecular film is either quenched or heavily altered due to: (i) molecule–surface interactions and (ii) differing intermolecular interactions in films relative to the bulk. By fabricating SCO complexes on a weakly interacting surface, the interfacial quenching problem is tackled. However, engineering intermolecular interactions in thin SCO active films is rather difficult. Here, a molecular self‐assembly strategy is proposed to fabricate thin spin‐switchable surface‐bound films with programmable intermolecular interactions. Molecular engineering of the parent complex system [Fe(H₂B(pz)₂)₂(bpy)] (pz = pyrazole, bpy = 2,2′‐bipyridine) with a dodecyl (C₁₂) alkyl chain yields a classical amphiphile‐like functional and vacuum‐sublimable charge‐neutral Fe^II complex, [Fe(H₂B(pz)₂)₂(C₁₂‐bpy)] (C₁₂‐bpy = dodecyl[2,2′‐bipyridine]‐5‐carboxylate). Both the bulk powder and 10 nm thin films sublimed onto either quartz glass or SiO_x surfaces of the complex show comparable spin‐state switching characteristics mediated by similar lamellar bilayer like self‐assembly/molecular interactions. This unprecedented observation augurs well for the development of SCO‐based applications, especially in molecular spintronics.     

Electric driven molecular switching of asymmetric tris(phthalocyaninato) lutetium triple-decker complex at the liquid/solid interface

Molecular structures are known to significantly impact the adsorption and assembling behavior of the adsorbates on surfaces. Precise control of the molecular orientation and ordering will enable us to tailor the physical and chemical properties of the molecular architectures. In this work, we present a strategy of attaching functional groups with dissimilar adsorption and assembling characteristics to the top and bottom phthalocyaninato moieties of a triple-decker complex, and orientational-dependent ordering of such molecules at the liquid/solid interface has been identified, which is attributed to the interaction of the intrinsic molecular dipole with the external electric field. In addition, isomerization of the noncentrosymmetric tris(phthalocyaninato) lutetium triple-decker complex has been revealed directly with STM and further confirmed by theoretical simulation. This approach provides a possible way for the preparation of organic films with switchable electronic and/or interface properties with external field.     

Factors affecting the adsorption of stabilisers on to carbon black (flow micro-calorimetry studies) Part III Surface activity study using acid/base model probes

The first and second part of this series of papers investigated the interaction between carbon black and stabilisers (phenolic antioxidants and HALS, respectively) and showed that the mechanism was dependent on both the chemical nature of the carbon black surface and the molecular structure of stabilisers. In this third part, the interactions between model compounds, of varying acidity, and the same four carbon blacks, are investigated using flow micro-calorimetry (FMC) and Fourier transform Infrared spectroscopy (FTIR). As with the first and second parts, differences in adsorption behaviour between the four types of carbon black were evident and were principally related to the chemical nature of the surfaces and the adsorbates. In this study further insight in to the nature of the interactions between the carbon black surface functional groups and the acidic and basic probes has been acquired. The main forms of interaction are hydrogen bonding and Lewis and Bronsted acid/base interactions, formation of proton transfer complexes was also considered possible in cases of strong adsorption. The adsorption behaviour of acid and basic aromatic probes, together with octadecanol and stearic acid, was also found to be dependant on the carbon black surface topography. Flat graphene layers containing minimal heteroatoms favoured adsorption of the latter species as flat adsorption and/or structural ordering was permissable.     

Organizational Structure and Electronic Decoupling of Surface Bound Chiral Domains and Biomolecules

For the development of reagentless biological and chemical species detection at the single molecule level using external fields, including terahertz radiation, it is paramount to study model systems that uncover how intermolecular and molecule-surface interactions dictate monolayer ordering and electronic properties. This paper addresses two types of molecule-surface interactions and two distinct molecular systems, both of which impact our fundamental understanding of confined molecular domains and single molecule detection. We will first discuss the ordering and electronic characteristics of a chiral molecule, tartaric acid , weakly bound to an achiral metal surface, Ag(111), as studied with low temperature scanning tunneling microscopy (STM). This particular molecule-surface system contains many key elements, including hydrogen bonding interactions and stereochemical features, that would be common to other functional detection schemes. This paper will also treat the characterization of isolated, thiolated DNA molecules chemically bound to Au(111) terraces. Ambient STM and atomic force microscopy (AFM) measurements of both short and long DNA structures in both single and double strand configurations will be discussed with particular attention paid to imaging mechanisms involved. These results are particularly relevant to systems involving biomolecules anchored to inert metal surfaces, such as those used in external field-based assays.     

Substrate Templating upon Self‐Assembly of Hydrogen‐Bonded Molecular Networks on an Insulating Surface

Molecular self‐assembly on insulating surfaces, despite being highly relvant to many applications, generally suffers from the weak molecule–surface interactions present on dielectric surfaces, especially when benchmarked against metallic substrates. Therefore, to fully exploit the potential of molecular self‐assembly, increasing the influence of the substrate constitutes an essential prerequisite. Upon deposition of terephthalic acid and trimesic acid onto the natural cleavage plane of calcite, extended hydrogen‐bonded networks are formed, which wet the substrate. The observed structural complexity matches the variety realized on metal surfaces. A detailed analysis of the molecular structures observed on calcite reveals a significant influence of the underlying substrate, clearly indicating a substantial templating effect of the surface on the resulting molecular networks. This work demonstrates that choosing suitable molecule/substrate systems allows for tuning the balance between intermolecular and molecule–surface interactions even in the case of typically weakly interacting insulating surfaces. This study, thus, provides a strategy for deliberately exploiting substrate templating to increase the structural variety in molecular self‐assembly on a bulk insulator at room temperature.     

Controlling the assembly of hydrophobized gold nanoparticles at the air-water interface by varying the interfacial tension

Controlled assembly is the key to harness the nanoscale properties of nanoparticles in most technological applications and it has been an important challenge as it leads to the manipulation of interparticle properties. The present work depicts the control of the assembly of nanoparticles in the monolayers by evaporation kinetics and particle interactions at the air-liquid interface. In the presence of attractive particle-particle and particle-monolayers interactions, nanoparticles self assemble into a superlattice structure upon drying from a colloidal suspension on to the preformed lipid monolayers. This self-assembly mechanism produces monolayers with long-range ordering. However, rapid dewetting and high rate of evaporation can significantly undermine the extent of ordering. Using gold nanoparticles as vehicles for experimentation and by changing the monolayers and solvent, we here demonstrate that the extent of ordering of nanoparticles can be controlled.     

Orientational Ordering of Electric Quadrupoles in FCC Lattices

Rigid rotors with electric quadrupole moment which are localized at FCC lattice sites have been studied by Monte Carlo simulations. It is found that as the temperature lowers the classical rotors are orientationally ordered to form a Pa3 structure. Molecular solids of nitrogen and orthohydrogen were observed to show this orientational ordering at low temperatures, which is understood to be due to the anisotropic interactions between the molecules. Since most of the anisotropy in the intermolecular interactions can be explained by electric quadrupole-quadrupole interaction, we compare our calculation with the experimental results for solid N₂ and ortho-H₂.      

Triphenylene‐Derived Electron Acceptors and Donors on Ag(111): Formation of Intermolecular Charge‐Transfer Complexes with Common Unoccupied Molecular States

Over the past years, ultrathin films consisting of electron donating and accepting molecules have attracted increasing attention due to their potential usage in optoelectronic devices. Key parameters for understanding and tuning their performance are intermolecular and molecule–substrate interactions. Here, the formation of a monolayer thick blend of triphenylene‐based organic donor and acceptor molecules from 2,3,6,7,10,11‐hexamethoxytriphenylene (HAT) and 1,4,5,8,9,12‐hexaazatriphenylenehexacarbonitrile (HATCN), respectively, on a silver (111) surface is reported. Scanning tunneling microscopy and spectroscopy, valence and core level photoelectron spectroscopy, as well as low‐energy electron diffraction measurements are used, complemented by density functional theory calculations, to investigate both the electronic and structural properties of the homomolecular as well as the intermixed layers. The donor molecules are weakly interacting with the Ag(111) surface, while the acceptor molecules show a strong interaction with the substrate leading to charge transfer and substantial buckling of the top silver layer and of the adsorbates. Upon mixing acceptor and donor molecules, strong hybridization occurs between the two different molecules leading to the emergence of a common unoccupied molecular orbital located at both the donor and acceptor molecules. The donor acceptor blend studied here is, therefore, a compelling candidate for organic electronics based on self‐assembled charge‐transfer complexes.     

Nano-architectures by covalent assembly of molecular building blocks

The construction of electronic devices from single molecular building blocks, which possess certain functions such as switching or rectifying and are connected by atomic-scale wires on a supporting surface, is an essential goal of molecular electronics. A key challenge is the controlled assembly of molecules into desired architectures by strong, that is, covalent, intermolecular connections, enabling efficient electron transport between the molecules and providing high stability. However, no molecular networks on surfaces 'locked' by covalent interactions have been reported so far. Here, we show that such covalently bound molecular nanostructures can be formed on a gold surface upon thermal activation of porphyrin building blocks and their subsequent chemical reaction at predefined connection points. We demonstrate that the topology of these nanostructures can be precisely engineered by controlling the chemical structure of the building blocks. Our results represent a versatile route for future bottom-up construction of sophisticated electronic circuits and devices, based on individual functionalized molecules.     

The Stability of Drug Adsorbates on Silica

Colloidal and porous silicas are used as carriers in solid, semisolid and liquid dosage forms. Adsorption of active ingredients onto their large surface areas can be used to regulate drug release or for the uniform distribution of drug in single dose units with a very low drug content. In the adsorbates the contact between drug and carrier surface on the molecular level can be of great importance for the chemical stability of drug preparations. This is demonstrated by the following examples:

Hydrolytic degradation of acetyl salicylic acid in dry silica adsorbates is mainly determined by alkaline impurities of the carrier and strongly adsorbed water on the silica surface. The “catalytic” action of silicas is, therefore, directly dependent on the preparation technique of the carrier. Propantheline a cationic ester compound is adsorbed on silica from aqueous solution. In aqueous silica suspensions and in dry adsorbates the ester hydrolysis is controlled by the pH, the neutral salt content, and buffer substances, due to different adsorption mechanisms.

The oxidative degradation of butylhydroxyanisole in silica adsorbates was also found to be enhanced in the presence of alkaline impurities. The oxidation of linoleic acid methylester in oleogels of colloidal silica proved to be influenced both by carrier impurities and the specific adsorption of intermediates (peroxides) onto the surface.     

High-sensitivity stark spectroscopy obtained by surface plasmon resonance measurement

The effect (Stark effect) of an applied electric field on the electronic states of molecular adsorbates was studied by measuring surface plasmon resonance (SPR) as a function of the wavelength of the incident light that excites the SPR. Using the Kramers-Kronig relation, Stark spectra comparable to those obtained with conventional methods were extracted from the electric field-induced SPR angular shift for several organic adsorbates. Because this method relies on detecting the SPR angular shift that can be measured precisely, high-sensitivity Stark spectroscopy can be achieved. In addition, the adsorbate coverage information can be determined from the SPR angular shift upon molecular adsorption.     

改性介孔无机凝胶的制备及其在溶液中的吸附机理

未改性的介孔无机凝胶虽然具有较大的孔径,原则上可以吸附较大的分子或离子,但由于吸附剂的表面性质简单,与吸附质之间的作用力弱,因而吸附容量低,选择性不理想.采用表面修饰或杂化的方法在介孔凝胶中引入各种官能团或改变介孔凝胶的表面电荷之后,吸附剂的表面性质得到了很大的改善,吸附剂可以靠静电作用、离子交换、疏水作用、氢键、络合作用、基于分子阀门的开关效应和基于分子印迹的分子识别等机制对吸附质进行选择吸附.     

Reprogrammable Assembly of Molecular Motor on Solid Surfaces via Dynamic Bonds

Controllable assembly of molecular motors on solid surfaces is a fundamental issue for providing them to perform physical tasks. However, it can hardly be achieved by most previous methods due to their inherent limitations. Here, a general strategy is designed for the reprogrammable assembly of molecular motors on solid surfaces based on dynamic bonds. In this method, molecular motors with disulfide bonds can be remotely, reversibly, and precisely attached to solid surfaces with disulfide bonds, regardless of their chemical composition and microstructure. More importantly, it not only allows encoding geometric information referring to a pattern of molecular motors, but also enables erasing and re‐encoding of geometric information via hemolytic photocleavage and recombination of disulfide bonds. Thus, solid surfaces can be regarded as “computer hardware”, where molecular motors can be reformatted and reprogramed as geometric information.     

Some Remarks on the Viscometric Behaviour of the Systems Couplers-Gelatin and Couplers-Synthetic Polymers

Some aspects of the mechanism of the interactions between nondiffusing couplers and gelatin or hydrophilic synthetic polymers were investigated by viscometry, studying (a) the role played by the polymer; (b) the effect of the solvent; (c) the influence of operative factors.

The interactions between the polymers and the couplers examined depended on the type, molecular size and structure of the polymer and on the chemical structure of the coupler. In most cases a threshold polymer concentration was found, above which the interactions began to be evident.

Polar surface active solvents seem to interact with the coupler aliphatic side chain, hindering the coiling up of the polymer- coupler aggregates, while pre-warming of the samples hinders the building up of intermolecular aggregates.

An ageing effect of the polymer-coupler solutions was detected, which probably means that the aggregates undergo some structural and configurational changes during the storage time.     

Spontaneous assembly of viruses on multilayered polymer surfaces

The idea that randomly arranged supermolecular species incorporated in a network medium can ultimately create ordered structures at the surface may be counterintuitive. However, such order can be accommodated by regulating dynamic and equilibrium driving forces. Here, we present the ordering of M13 viruses, highly complex biomacromolecules, driven by competitive electrostatic binding, preferential macromolecular interactions and the rigid-rod nature of the virus systems during alternating electrostatic assembly. The steric constraints inherent to the competitive charge binding between M13 viruses and two oppositely charged weak polyelectrolytes leads to interdiffusion and the virtual 'floating' of viruses to the surface. The result is the spontaneous formation of a two-dimensional monolayer structure of viruses atop a cohesive polyelectrolyte multilayer. We demonstrate that this viral-assembled monolayer can be a biologically tunable scaffold to nucleate, grow and align nanoparticles or nanowires over multiple length scales. This system represents an interface that provides a general platform for the systematic incorporation and assembly of organic, biological and inorganic materials.     

Altering the ordering and disordering of a triangular nanographene at room temperature

Molecular self-organization has the potential to serve as an efficient and versatile tool for the spontaneous creation of low-dimensional nanostructures on surfaces. We demonstrate how the subtle balance between intermolecular interactions and molecule-surface interactions can be altered by modifying the environment or through manipulation by means of the tip in a scanning tunnelling microscope (STM) at room temperature. We show how this leads to the distinctive ordering and disordering of a triangular nanographene molecule, the trizigzag-hexa-peri-hexabenzocoronenes-phenyl-6 (trizigzagHBC-Ph6), on two different surfaces: graphite and Au(111). The assembly of submonolayer films on graphite reveals a sixfold packing symmetry under UHV conditions, whereas at the graphite-phenyloctane interface, they reorganize into a fourfold packing symmetry, mediated by the solvent molecules. On Au(111) under UHV conditions in the multilayer films we investigated, although disorder prevails with the molecules being randomly distributed, their packing behaviour can be altered by the scanning motion of the tip. The asymmetric diode-like current-voltage characteristics of the molecules are retained when deposited on both substrates. This paper highlights the importance of the surrounding medium and any external stimulus in influencing the molecular organization process, and offers a unique approach for controlling the assembly of molecules at a desired location on a substrate.     

Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State

Controlled self‐assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self‐assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral–zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion‐containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge‐driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid–graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.