Analysis of van der Waals loops in the adsorption isotherms of porous systems

The properties of the van der Waals loops for isotherms of the adsorbate located in the slit-shaped and cylindrical pores of different width were analyzed. The adsorbate molecules are modeled by spherical Lennard-Jones type particles. The calculation was based on the latticegas model in the quasichemical approximation for intermolecular interactions. The accuracy of calculations of the adsorption hysteresis loops increases due to the use of distributed models, which reflect the spatial inhomogeneity of the distribution of molecules along the normal to the pore wall. The effect of the adsorbate-adsorbent interaction potential and pore width on the pattern of adsorption isotherms is considered. Taking into account the inhomogeneity of the spatial distribution of molecules changes the course of the spinodal sections of the adsorption isotherms.     

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 benzene on coinage metals: a theoretical analysis using wavefunction-based methods

The interaction of benzene with a Ag(111) surface has been determined using reliable ab initio electronic structure calculations. The results are compared to a recent detailed analysis of the interaction of benzene with copper and gold surfaces, thus making it possible to derive a consistent picture for the electronic structure changes encountered when benzene is brought into contact with the densely packed coinage metal surfaces. To avoid the problems encountered when the presently most frequently employed computational approach, density functional theory (DFT), is applied to adsorbate systems where dispersion (or van der Waals) forces contribute substantially, we use a wavefunction-based approach. In this approach, the weak van der Waals interactions, which are dominated by correlation effects, are described using second-order perturbation theory. The surface dipole moment and the work function changes induced upon adsorption are also discussed.     

Density functional theory investigation of benzenethiol adsorption on Au(111)

We have studied the adsorption of benzenethiol molecules on the Au(111) surface by using first principles total energy calculations. A single thiolate molecule is adsorbed at the bridge site slightly shifted toward the fcc-hollow site, and is tilted by 61 degrees from the surface normal. As for the self-assembled monolayer (SAM) structures, the (2 square root of 3 x square root of 3)R30 degrees herringbone structure is stabilized against the (square root 3 x square root 3)R30 degrees structure by large steric relaxation. In the most stable (2 square root 3 x square root 3)R30 degrees SAM structure, the molecule is adsorbed at the bridge site with the tilting angle of 21 degrees, which is much smaller compared with the single molecule adsorption. The van der Waals interaction plays an important role in forming the SAM structure. The adsorption of benzenethiolates induces the repulsive interaction between surface Au atoms, which facilitates the formation of surface Au vacancy.     

Information from IR fundamental and overtone spetra of diatomics adsorbed in zeolites NaCaA

From fundamental and overtone spectra of CO, NO and D₂ adsorbed in zeolites NaCaA the constants of the internuclear potential can be derived for the adsorbed state. As the interactions with the zeolite surface are dominated by van der Waals forces, they remain less affected by adsorption. In contrast to diatomics adsorbed on transition metal surfaces, no considerable alteration of bond energy can be observed. The frequency shift is essentially due to the change of the harmonic force constant and indicates the interaction potential depending almost linearly on the vibrational state. The heterogeneity of the cation distribution inside the zeolites is reflected in the broadening of the adsorbate bands.     

Many-body response of benzene at monolayer MoS2: Van der Waals interactions and spectral broadening

Models of surface enhancement of molecular electronic response properties are challenging for two reasons: (a) molecule-surface interactions require a simultaneous solution of the molecular and the surface dynamic response (a daunting task), and (b) when solving for the electronic structure of the combined molecule + surface system, it is not trivial to single out the particular physical effects responsible for enhancement. To tackle this problem, in this work, we apply a formally exact decomposition of the system's response function into subsystem contributions by using subsystem density functional theory (DFT), which grants access to dynamic polarizabilities and optical spectra. In order to access information about the interactions between the subsystems, we extend a previously developed subsystem-based adiabatic connection fluctuation-dissipation theorem of DFT to separate the additive from the nonadditive correlation energy and identify the nonadditive correlation as the van der Waals interactions. As an example, we choose benzene adsorbed on monolayer MoS₂. We isolate the contributions to benzene's dynamic response arising from the interaction with the surface, and for the first time, we evaluate the enhancements to the effectiveness of C₆ coefficients as a function of benzene-MoS₂ distance and adsorption site. We also quantify the spectral broadening of the benzene's electronic excited states due to their interaction with the surface. We find that the broadening has a similar decay law with the molecule-surface distance as the leading van der Waals interactions (ie, R⁻⁶ ) and that the surface enhancement of dispersion interactions between benzene molecules is less than 5% but is still large enough (0.5 kcal/mol) to likely play a role in the prediction of interface morphologies.     

Weakly interacting molecular layer of spinning C60 molecules on TiO2 (110) surfaces

The adsorption of C(60), a typical acceptor organic molecule, on a TiO(2) (110) surface has been investigated by a multitechnique combination, including van der Waals density functional calculations. It is shown that the adsorbed molecules form a weakly interacting molecular layer, which sits on the fivefold-coordinated Ti that is confined between the prominent bridging oxygen rows (see figure).     

New method to measure packing densities of self-assembled thiolipid monolayers

For a monolayer of 2,3-di-phytanyl-sn-glycerol-1-tetraethylene glycol-D,L-a-lipoic acid ester lipid (DPTL) self-assembled (SAM) at a gold electrode surface we propose a new method to determine the charge number per adsorbed molecule and the packing density (area per molecule) in the monolayer. The method relies on chronocoulometry to measure the charge density at the SAM covered gold electrode surface. Two series of measurements have to be performed. In the first series, charge densities are measured for a monolayer transferred from the air-solution to the metal-solution interface using the Langmuir-Blodgett (LB) technique. This series of measurements allows one to determine charge numbers per adsorbed DPTL molecule. The second series is performed using a gold electrode covered with a self-assembled monolayer. The charge densities obtained in this series are then used to calculate the packing density with the help of charge numbers per adsorbed DPTL determined in the first series. The area per adsorbed molecule determined by the new method was compared to the area per molecule determined by the popular reductive desorption method. The molecular area determined with the new method is about 20% larger than the area calculated from the van der Waals model, which is a physically reasonable result. In contrast, the popular reductive desorption method gives an area per molecule 20% lower than the minimum estimated based on a van der Waals model. This is a physically unreasonable result. It is also shown that the charge numbers per adsorbed molecule depend on the electrode potential and may assume values smaller than the number of electrons participating in the reductive desorption step. An explanation of the origin of the "partial charge numbers" is provided. We recommend the new method be used in future studies of thiol adsorption at metal surfaces.     

非手性的酞菁铜分子在Bi(111)表面上的手性特征

利用低温扫描隧道显微镜（LT-STM）研究了酞菁铜（CuPc）分子在Bi（111）表面上的吸附和手性自组装结构。由于较弱的分子-衬底相互作用,我们发现在液氮温度（78 K）下吸附在Bi（111）表面上的单个CuPc分子围绕着分子中心发生旋转,直到遇到其他分子形成团簇为止。随着分子覆盖度的增加,CuPc分子形成了自组装分子单层。高分辨STM图表明,非手性的CuPc分子出现了手性特征：两个相对的酞菁基团发生了弯曲。当覆盖度超过一个分子层,酞菁铜分子的吸附取向由“平躺”转变到“站立”姿态。我们认为,酞菁铜分子的手性起源是由两种因素共同导致的结果：一种是分子-衬底之间的非对称电荷转移,另一种是相邻分子间的非对称性的范德华力作用。     

Anisotropic adsorption of molecular assemblies on crystalline surfaces

Orientational order of surfactant micelles and proteins on crystalline templates has been observed but, given that the template unit cell is significantly smaller than the characteristic size of the adsorbate, this order cannot be attributed to lattice epitaxy. We interpret the template-directed orientation of rodlike molecular assemblies as arising from anisotropic van der Waals interactions between the assembly and crystalline surfaces where the anisotropic van der Waals interaction is calculated using the Lifshitz methodology. Provided the assembly is sufficiently large, substrate anisotropy provides a torque that overcomes rotational Brownian motion near the surface. The probability of a particular orientation is computed by solving a Smoluchowski equation that describes the balance between van der Waals and Brownian torques. Torque aligns both micelles and protein fibrils; the interaction energy is minimized when the assembly lies perpendicular to a symmetry axis of a crystalline substrate. Theoretical predictions agree with experiments for both hemi-cylindrical micelles and protein fibrils adsorbed on graphite.     

Two-dimensional molecular sieves: structure design by computer simulations

Nanoporous molecular networks formed spontaneously by organic molecules adsorbed on solid substrates are promising materials for future nanotechnological applications related to separation and catalysis. With their unique ordered structure comprising nanocavities of a regular shape planar networks can be treated as 2D analogs of bulk nanoporous materials. In this report we demonstrate how the Monte Carlo simulation method can be effectively used to predict morphology of self-assembled porous molecular architectures based on structural properties of a building block. The simulated results refer to the assemblies created by cross-shaped organic molecules which are stabilized by different intermolecular interactions, including hydrogen bonding and van der Waals interactions. It is demonstrated that tuning of size and aspect ratio of the building block enables the creation of largely diversified extended structures comprising pores of a square and rectangular shape. Our theoretical predictions can be helpful in custom design of functional adsorbed overlayers for controlled deposition, sensing and separation of guest molecules.     

Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.     

Monte Carlo simulations of antibody adsorption and orientation on charged surfaces

Monte Carlo simulations were performed to study the adsorption and orientation of antibodies on charged surfaces based on both colloidal and all-atom models. The colloidal model antibody consists of 12 connected beads representing the 12 domains of an antibody molecule. The structure of the all-atom antibody model was taken from the protein databank. The effects of the surface charge sign and density, the solution pH and ionic strength on the adsorption and orientation of different colloidal model antibodies with different dipole moments were examined. Simulation results show that both the 12-bead and the all-atom models of the antibody, for which the dipole moment points from the Fc to (Fab)2 fragments, tend to have the desired "end-on" orientation on positively charged surfaces and undesired "head-on" orientation on negatively charged surfaces at high surface charge density and low solution ionic strength where electrostatic interactions dominate. At low surface charge density and high solution ionic strength where van der Waals interactions dominate, 12-bead model antibodies tend to have "lying-flat" orientation on surfaces. The orientation of adsorbed antibodies results from the compromise between electrostatic and van der Waals interactions. The dipole moment of an antibody is an important factor for antibody orientation on charged surfaces when electrostatic interactions dominate. This charge-driven protein orientation hypothesis was verified by our simulations results in this work. It was further confirmed by surface plasmon resonance biosensor and time-of-flight secondary ion mass spectrometry experiments reported elsewhere.     

Thermodynamic and orientational properties of two-dimensional multicomponent hard rectangle fluids

A molecular statistical model is developed for a two-dimensional multicomponent fluid composed of hard rectangles. The configurational partition function of such a system on a square lattice is evaluated by applying the orientation dependent version of the Flory-Huggins probability method. Unlike earlier treatments of similar problems, the final result for the configurational entropy is independent of the order of placement of the rectangular plate-like particles. The present approach has been extended to enable an analysis of both facewise and edgewise modes of adsorption of rectangular molecules on a planar surface. Further, the limit of infinitesimal lattice size has been considered as the generalized continuous version of the corresponding lattice model. The results obtained within the present continuous approach are compared with those of studies of related one-component hard body fluids.     

Thermodynamic and orientational properties of two-dimensional multicomponent hard rectangle fluids

A molecular statistical model is developed for a two-dimensional multicomponent fluid composed of hard rectangles. The configurational partition function of such a system on a square lattice is evaluated by applying the orientation dependent version of the Flory-Huggins probability method. Unlike earlier treatments of similar problems, the final result for the configurational entropy is independent of the order of placement of the rectangular plate-like particles. The present approach has been extended to enable an analysis of both facewise and edgewise modes of adsorption of rectangular molecules on a planar surface. Further, the limit of infinitesimal lattice size has been considered as the generalized continuous version of the corresponding lattice model. The results obtained within the present continuous approach are compared with those of studies of related one-component hard body fluids.     

酪氨酸在活性炭/水界面上的吸附

研究了不同pH值介质中酪氨酸在活性炭上的吸附行为.结果表明,pH值4.2～6.1时吸附量较大,在酪氨酸的等电点时吸附量最大;酪氨酸被吸附的主要形式是兼性离子;酪氨酸离子靠VanderWaals力吸附在活性炭/水界面上.用介质pH值对酪氨酸溶解度的影响和活性炭的表面性质解释了实验结果     

Hydrogen-bonding versus van der Waals interactions in self-assembled monolayers of substituted isophthalic acids

Self-assembled monolayers of a series of isophthalic acids (5-octadecyloxyisophthalic acid, 5-decyloxyisophthalic acid, 5-hexyloxyisophthalic acid, and 5-pentyloxyisophthalic acid) formed on highly ordered pyrolytic graphite (HOPG) at the solid-liquid interface were studied using scanning tunneling microscopy (STM). Although these molecules have the same dicarboxyl headgroup, their hydrocarbon tails are of different lengths. Hydrogen-bonding between headgroups and van der Waals interactions between the hydrocarbon tails control the final morphology of the monolayer. The STM images show that both van der Waals interactions (vdWs) and hydrogen-bonding (H-B) compete to control the structure, but the final structure of the monolayer is determined by balance between the two interactions.     

聚苯乙烯在石墨表面吸附的分子动力学模拟

采用分子动力学(MD)模拟方法研究了单链聚苯乙烯(PS)在石墨表面的吸附. 模拟结果表明, 吸附后PS在平行于石墨表面的方向可视为准二维椭圆结构, 并且在此方向上的均方回转半径值(R2∥)与其所含单体数目(N)具有指数关系R2∥-N2v, 指数2v约等于1.04; 最后指出PS吸附过程的主要驱动力为PS链段与表面之间的范德华作用力.     

Simple model for DNA adsorption onto a mica surface in 1:1 and 2:1 electrolyte solutions

We propose a simple theory of interactions between like-charged polyelectrolyte and a surface based on a mean-field Derjaguin-Landau-Verwey-Overbeek approach. It predicts that the van der Waals attractive interactions are responsible for irreversible physisorption of polyelectrolytes onto charged surfaces. We show that monovalent salts contribute significantly to repulsive interactions, while enhancing the attraction very slightly. The effect of the divalent counterions is reverse. Therefore, to achieve the adsorption, the overall repulsion due to 1:1 electrolyte should be counterbalanced by the stronger van der Waals attraction due to the presence of doubly charged counterions in solution. The theory has been validated experimentally against its ability to predict the minimum polymer/surface interaction energy required for the adsorption using DNA/mica in NaCl, MgCl2, and NiCl2 solutions as a test system. The theory explains the mechanism of linear DNA adsorption to a mica surface for different solvent compositions and can be used as a tool for predicting the optimum conditions for AFM experiments on linear polymer systems. The model can also be used to make general conclusions on the conformation of polymer molecules on a surface. We have shown for the DNA/mica surface system that when the adsorption of DNA is mostly governed by long-range van der Waals forces the molecule adopts an ideal 2D conformation. When the adsorption is mostly due to short-range ion-correlation forces, DNA will appear 3D --> 2D projected in agreement with experimental data.     

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.