Modulating the self-assembly of rigid "clicked" dendrimers at the solid-liquid interface by tuning non-covalent interactions between side groups

First generation poly(triazole-phenylene) dendrimers equipped with peripheral alkyl or carboxylic acid groups to engage in van der Waals and hydrogen-bonding interactions, respectively, assemble into distinct two-dimensional nano-structures at the solid-liquid interface as revealed by high resolution STM investigations.     

Hydrogen bonding versus van der Waals interactions: competitive influence of noncovalent interactions on 2D self-assembly at the liquid-solid interface

The structures of the self-assembled monolayers of various 4-alkoxybenzoic acids physisorbed at the liquid-solid interface were established by employing scanning tunnelling microscopy (STM). This study has been essentially undertaken to explore the competitive influence of van der Waals and hydrogen-bonding interactions on the process of two-dimensional self-assembly. These acid derivatives form hydrogen-bonded dimers as expected; however, the dimers organise themselves in the form of relatively complex lamellae. The characteristic feature of these lamellae is the presence of regular discommensurations or kinks along the lamella propagation direction. The formation of kinked lamellae is discussed in light of the registry mechanism of the alkyl chains with the underlying graphite substrate. The location of the kinks along a lamella depends on the number (odd or even) of carbon atoms in the alkyl chain. This result indicates that concerted van der Waals interactions of the alkyl chain units introduce the odd/even chain-length effect on the surface-assembled supramolecular patterns. The odd/even effects are retained even upon complexation with a hydrogen-bond acceptor. However, as the solvent is changed from 1-phenyloctane to 1-octanoic acid, the kinked lamellae as well as the odd/even effects disappear. This solvent-induced convergence of supramolecular patterns is attained by means of co-crystallisation of octanoic acid molecules in the 2D crystal lattice, which is evident from high-resolution STM images. The solvent co-adsorption phenomenon is discussed in terms of competing van der Waals and hydrogen-bonding interactions.     

Synthesis of dehydrobenzo[18]annulene derivatives and formation of self-assembled monolayers: implications of core size on alkyl chain interdigitation

The synthesis of a series of dodecadehydrotribenzo[18]annulene ([18]DBA) derivatives is reported, together with their steady-state absorption and fluorescence properties. The main focus, though, is on the self-assembly of these compounds at the liquid-solid interface as investigated with scanning tunneling microscopy (STM), highlighting the effect of alkyl chain orientation and alkyl chain length on the molecular ordering. Owing to the large triangular pi-electron system of the [18]DBAs, two different types of alkyl chain orientation are observed. The observed changes in the monolayer networks upon elongation of the alkyl chains are attributed to the increased van der Waals interactions between molecules and substrate. The effect of the core size on the alkyl chain orientation and, as a result, the monolayer structure is discussed in relation to the results obtained previously for triangularly-shaped dehydrobenzo [12]annulene ([12]DBA) derivatives and triphenylene derivatives. A guideline for substituent spacing allowing control of molecular alignment for large planar pi-electron systems utilizing directional alkyl chain interdigitation is also discussed.     

吡嗪衍生物在石墨表面上的自组装单层膜结构

利用扫描隧道显微镜研究了荧光液晶分子2, 5-二-[2-(3, 4-二-十二烷氧基-苯基)-乙烯基]-3, 6-二甲基吡嗪(BPDP12)在石墨表面上自组装单层膜的结构. 实验结果表明, 该化合物在石墨表面形成两种自组装结构：一种是稳定的, 分子的共轭中心相互平行, 烷基链相互交错的密排结构；另一种是不稳定的, 分子的共轭中心彼此为烷基链所分隔的非密排结构. 分子之间较强的π-π作用和分子烷基链之间的范德华作用力对分子组装的取向形成竞争, 是产生两种不同组装结构的根本原因.     

Two-dimensional self-assembly of a two-component molecular system: formation of an ordered and homogeneous molecular mesh

The formation of nanoscaled objects often relies on the two-dimensional self-assembly of organic molecules on solid substrates, leading to a number of interesting structures with nanometer dimensions. Assembly of single-component systems driven by chain-chain van der Waals interactions, hydrogen bonding, and dipolar interactions governs the structures typically formed. The two-dimensional self-assembly of a two-component molecular system is described here, where the structure involves mixing of the components at the molecular level. A mixture of 5-octadecyloxyisophthalic acid and octanoic acid forms an ordered stoichiometric array of homogeneous nanometer-sized openings of dimension 8.5 A x 13.5 A x1.8 A, verified by atomic resolution scanning tunneling microscopy. Assembly in the structure is driven by van der Waals and hydrogen bonding interactions between the molecular components.     

Subsurface influence on the structure of protein adsorbates as revealed by in situ X-ray reflectivity

The adsorption process of proteins to surfaces is governed by the mutual interactions among proteins, the solution, and the substrate. Interactions arising from the substrate are usually attributed to the uppermost atomic layer. This actual surface defines the surface chemistry and hence steric and electrostatic interactions. For a comprehensive understanding, however, the interactions arising from the bulk material also have to be considered. Our protein adsorption experiments with globular proteins (α-amylase, bovine serum albumin, and lysozyme) clearly reveal the influence of the subsurface material via van der Waals forces. Here, a set of functionalized silicon wafers enables a distinction between the effects of surface chemistry and the subsurface composition of the substrate. Whereas the surface chemistry controls whether the individual proteins are denatured, the strength of the van der Waals forces affects the final layer density and hence the adsorbed amount of proteins. The results imply that van der Waals forces mainly influence surface processes, which govern the structure formation of the protein adsorbates, such as surface diffusion and spreading.     

Adsorption of square and rectangular plate-like molecules on a planar surface

A mean-field statistical thermodynamic analysis of monolayer adsorption of rigid square and rectangular plate-like molecules on a homogeneous planar surface is developed. The analysis is simplified by only considering facewise and edgewise modes of adsorption in restricted orthogonal orientations parallel to the surface. The free energy density, adsorbate population distribution and surface spreading pressure are obtained as a function of adsorbate density and compared for square plate molecules using three different sequences of adsorbate molecule placement on the surface to evaluate the configurational degeneracy. It is found that edgewise adsorbed molecules can be anisotropically ordered if the edge length of square and rectangular plate-like molecules exceeds three length units in the absence of anisotropic dispersion interactions. If intermolecular dispersion interactions are present and of sufficient strength, the spreading pressure-density isotherms can exhibit one or two van der Waals loops for square plate molecules with three van der Waals loops possible for rectangular plate adsorbate molecules. The phase transitions for the adsorbed monolayer corresponding to the appearance of these van der Waals loops are discussed.     

Nonadditivity in van der Waals interactions within multilayers

Working at the macroscopic continuum level, we investigate effective van der Waals interactions between two layers within a multilayer assembly. By comparing the pair interactions between two layers with effective pair interactions within an assembly we assess the significant consequences of nonadditivity of van der Waals interactions. This allows us to evaluate the best numerical estimate to date for the Hamaker coefficient of van der Waals interactions in lipid-water multilamellar systems.     

Van der Waals Emulsions: Emulsions Stabilized by Surface‐Inactive,Hydrophilic Particles via van der Waals Attraction

Surface‐inactive, highly hydrophilic particles are utilized to effectively and reversibly stabilize oil‐in‐water emulsions. This is a result of attractive van der Waals forces between particles and oil droplets in water, which are sufficient to trap the particles in close proximity to oil–water interfaces when repulsive forces between particles and oil droplets are suppressed. The emulsifying efficiency of the highly hydrophilic particles is determined by van der Waals attraction between particle monolayer shells and oil droplets enclosed therein and is inversely proportional to the particle size, while their stabilizing efficiency is determined by van der Waals attraction between single particles and oil droplets, which is proportional to the particle size. This differentiation in mechanism between emulsification and stabilization will significantly advance our knowledge of emulsions, thus enabling better control and design of emulsion‐based technologies in practice.     

Van der Waals Emulsions: Emulsions Stabilized by Surface‐Inactive,Hydrophilic Particles via van der Waals Attraction

Surface‐inactive, highly hydrophilic particles are utilized to effectively and reversibly stabilize oil‐in‐water emulsions. This is a result of attractive van der Waals forces between particles and oil droplets in water, which are sufficient to trap the particles in close proximity to oil–water interfaces when repulsive forces between particles and oil droplets are suppressed. The emulsifying efficiency of the highly hydrophilic particles is determined by van der Waals attraction between particle monolayer shells and oil droplets enclosed therein and is inversely proportional to the particle size, while their stabilizing efficiency is determined by van der Waals attraction between single particles and oil droplets, which is proportional to the particle size. This differentiation in mechanism between emulsification and stabilization will significantly advance our knowledge of emulsions, thus enabling better control and design of emulsion‐based technologies in practice.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

Self-assembled organogels based on two-component system

Organogels were produced by the self-assembly of two organogelators, 3,5-bis(dodecanoylamino)benzoic acid and aromatic amines, in nonaromatic hydrocarbon solvents, through hydrogen bonding, aromatic stacking, and van der Waals interactions. 3,5-Bis(dodecanoylamino)benzoic acid has one carboxylic acid group for hydrogen bonding with amines and two alkylamide groups that can participate in interlayer hydrogen bonding and van der Waals interactions. The shape and size of the aromatic amines have a significant effect on the gel properties as well as their structures. A variety of organogels were realized by forming complexes of 3,5-bis(dodecanoylamino)benzoic acid and various amines with an aromatic group in nonaromatic hydrocarbon solvents.     

Specific and nonspecific interaction forces between Escherichia coli and silicon nitride, determined by poisson statistical analysis

The nature of the physical interactions between Escherichia coli JM109 and a model surface (silicon nitride) was investigated in water via atomic force microscopy (AFM). AFM force measurements on bacteria can represent the combined effects of van der Waals and electrostatic forces, hydrogen bonding, steric interactions, and perhaps ligand-receptor type bonds. It can be difficult to decouple these forces into their individual components since both specific (chemical or short-range forces such as hydrogen bonding) and nonspecific (long-range colloidal) forces may be present in the overall profiles. An analysis is presented based on the application of Poisson statistics to AFM adhesion data, to decouple the specific and nonspecific interactions. Comparisons with classical DLVO theory and a modified form of a van der Waals expression for rough surfaces were made in order to help explain the nature of the interactions. The only specific forces in the system were due to hydrogen bonding, which from the Poisson analysis were found to be -0.125 nN. The nonspecific forces of 0.155 nN represent an overall repulsive interaction. These nonspecific forces are comparable to the forces calculated from DLVO theory, in which electrostatic-double layer interactions are added to van der Waals attractions calculated at the distance of closest approach, as long as the van der Waals model for "rough" spherical surfaces is used. Calculated electrostatic-double layer and van der Waals interactions summed to 0.116 nN. In contrast, if the classic (i.e., smooth) sphere-sphere model was used to predict the van der Waals forces, the sum of electrostatic and van der Waals forces was -7.11 nN, which appears to be a large overprediction. The Poisson statistical analysis of adhesion forces may be very useful in applications of bacterial adhesion, because it represents an easy way to determine the magnitude of hydrogen bonding in a given system and it allows the fundamental forces to be easily broken into their components.     

Loosely packed self-assembled monolayer of N-hexadecyl-3,6-di(p-mercaptophenylacetylene)carbazole on gold and its application in biomimetic membrane research

Dithiols of N-hexadecyl-3,6-di(p-mercaptophenylacetylene)carbazole (HDMC) have been synthesized and employed to form self-assembled monolayers (SAMs) on gold. One characteristic of the HDMC molecule is its peculiar molecular structure consisting of a large and rigid headgroup and a small and flexible alkyl-chain tail. HDMC adsorbates can attach to gold substrates by a strong Au-S bond with weak van der Waals interactions between the alkyl-chain tails, leading to a loosely packed hydrophobic SAM. In this way we can couple hybrid bilayer membranes (HBMs) to gold surfaces with more likeness to a cell bilayer than the conventional HBMs based on densely packed long-chain alkanethiol SAMs. The insulating properties and stability of the HDMC monolayer as well as the HDMC/lipid bilayer on gold have been investigated by electrochemical techniques including cyclic voltammetry and impedance spectroscopy. To test whether the quality of the bilayer is sufficiently high for biomimetic research, we incorporated the pore-forming protein alpha-hemolysin) and the horseradish peroxidase into the bilayers, respectively. Experimental results demonstrated that this type of loosely packed hydrophobic SAM has great potential in biomimetic bilayer research and biosensor application.     

C-H/π-interaction-guided self-assembly in π-conjugated oligomers

We report CH/π hydrogen-bond-driven self-assembly in π-conjugated skeletons based on oligophenylenevinylenes (OPVs) and trace the origin of interactions at the molecular level by using single-crystal structures. OPVs were designed with appropriate pendants in the aromatic core and varied by hydrocarbon or fluorocarbon tails along the molecular axis. The roles of aromatic π-stack, van der Waals forces, fluorophobic effect and CH/π interactions were investigated on the theromotropic liquid crystallinity of OPV molecules. Single-crystal structures of hydrocarbon OPVs provided direct evidence for the existence of CH/π interactions between the π-ring (H-bond acceptor) and alkyl C-H (H-bond donor). The four important crystallographic parameters, d(c-x)=3.79 ?, θ=21.49°, φ=150.25° and d(Hp-x)=0.73 ?, matched in accordance with typical CH/π interactions. The CH/π interactions facilitate the close-packing of mesogens in x-y planes, which were further protruded along the c axis producing a lamellar structure. In the absence of CH/π interactions, van der Waals interactions drove the assembly towards a Schlieren nematic texture. Fluorocarbon OPVs exhibited smectic liquid-crystalline textures that further underwent Smectic A (SmA) to Smectic C (SmC) phase transitions with shrinkage up to 11%. The orientation and translational ordering of mesogens in the liquid-crystalline (LC) phases induced H- and J-type molecular arrangements in fluorocarbon and hydrocarbon OPVs, respectively. Upon photoexcitation, the H- and J-type molecular arrangements were found to emit a blue or yellowish/green colour. Time-resolved fluorescence decay measurements confirmed longer lifetimes for H-type smectic OPVs relative to that of loosely packed one-dimensional nematic hydrocarbon-tailed OPVs.     

Manipulation and characterization of xenon-metalloporphyrin complexation with a scanning tunneling microscope

The formation of a series of Xe-CuEtioI [Cu(II) etioporphyrin I] complexes on Cu(001) surface was identified by scanning tunneling microscopy (STM) at cryogenic condition. The binding sites of xenon to CuEtioI molecule were directly revealed by high-resolution STM images in combination with controlled manipulation. The interaction between xenon atoms and CuEtioI in the on-top configuration is suggestive of a charge-induced dipole interaction. The structural parameters obtained with the STM complement results from spectroscopic studies of van der Waals complexes.     

Structure and Molecular Recognition of Chiral Amino-Cyclodextrin: One-dimensional Array by Self-assembly in Solid and Chiral Discrimination in Solution

Abstract

The crystal structure and molecular recognition behaviour of a new chiral-amino cyclodextrin are reported; van der Waals interaction, hydrogen bond and the electrostatic interactions play an important role in the self-assembling process and chiral recognition for (R)-(-)-and (S)-(+)-mandelic acid.     

Delicate Balance of Non-Covalent Forces Govern the Biocompatibility of Graphitic Carbon Nitride towards Genetic Materials

Despite a plethora of suggested technological and biomedical applications, the nanotoxicity of two-dimensional (2D) graphitic carbon nitride (g-C₃N₄) towards biomolecules remains elusive. To address this issue, we employ all-atom classical molecular dynamics simulations and investigate the interactions between nucleic acids and g-C₃N₄. It is revealed that, toxicity is modulated through a subtle balance between electrostatic and van der Waals interactions. When the exposed nucleobases interact through predominantly short-ranged van der Waals and π–π stacking interactions, they get deviated from their native disposition and adsorb on the surface, leading to loss of self-stacking and intra-quartet H-bonding along with partial disruption of the native structure. In contrast, for the interaction with double-stranded structures of both DNA and RNA, long-range electrostatics govern the adsorption phenomena since the constituent nucleobases are relatively concealed and wrapped, thereby resulting in almost complete preservation of the nucleic acid structures. Construction of free energy landscapes for lateral translation of adsorbed nucleic acids suggests decent targeting specificity owing to their restricted movement on g-C₃N₄. The release times of nucleic acids adsorbed through predominant electrostatics are significantly less than those adsorbed through stacking with the surface. It is therefore proposed that g-C₃N₄ would induce toxicity towards any biomolecule having bare residues available for strong van der Waals and π–π stacking interactions relative to those predominantly interacting through electrostatics.     

Electronic structure and chemical bond in naphthalene and anthracene

We investigated the electronic structure of crystalline naphthalene and anthracene within the framework of density functional theory including van der Waals interactions (DFT-D). It is established that for better agreement with experimental values it is necessary to use the increased values of the van der Waals radii, which is caused by an overestimated value of the van der Waals interactions in crystalline linear oligoacenes. Utilization of the DFT-D leads to a correct account of the dispersion forces, which results in a high precision of the computed lattice parameters and cohesive energy. Based on the relaxed crystal structures, we have computed the total and deformation electron density and determined the mechanism of chemical bonds formation in crystals of naphthalene and anthracene. It has been established that the chemical bond in molecular crystals is formed under the influence of not only intramolecular but also intermolecular interactions. On the basis of the Mulliken population analysis it was revealed that two C(3) atoms in naphthalene (or C(3) and C(4) in anthracene) have a positive charge and the population of the rest of the carbon atoms increased, as compared with isolated molecule.