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.     

A modeling approach to describe the adhesion of rough, asymmetric particles to surfaces

A combined theoretical and experimental study of the adhesion of alumina particles and polystyrene latex spheres to silicon dioxide surfaces was performed. A boundary element technique was used to model electrostatic interactions between micron-scale particles and planar surfaces when the particles and surfaces were in contact. This method allows quantitative evaluation of the effects of particle geometry and surface roughness on the electrostatic interaction. The electrostatic interactions are combined with a previously developed model for van der Waals forces in particle adhesion. The combined model accounts for the effects of particle and substrate geometry, surface roughness and asperity deformation on the adhesion force. Predictions from the combined model are compared with experimental measurements made with an atomic force microscope. Measurements are made in aqueous solutions of varying ionic strength and solution pH. While van der Waals forces are generally dominant when particles are in contact with surfaces, results obtained here indicate that electrostatic interactions contribute to the overall adhesion force in certain cases. Specifically, alumina particles with complex geometries were found to adhere to surfaces due to both electrostatic and van der Waals interactions, while polystyrene latex spheres were not affected by electrostatic forces when in contact with various surfaces.     

Modeling van der Waals interactions between proteins and inorganic surfaces from time-dependent density functional theory calculations

In this work we show how the ab initio determination of van der Waals coefficients within time-dependent density functional theory can be used to build efficient and accurate atomistic models that describe the long-range interactions of proteins with other proteins and of proteins with semi-conducting surfaces. The model parameters are fitted so that they reproduce the ab initio van der Waals coefficients of amino acids and dipeptides. We then assess the quality of our results by comparing ab initio van der Waals coefficients for larger peptides with the coefficients yielded by the models. The different sets of parameters can be easily incorporated in current empirical force field methods, thus providing an essential ingredient for molecular dynamics simulations of proteins close to surfaces.     

Optical Trapping of Titania/Silica Core-Shell Colloidal Particles

Manipulation of colloidal systems via optical trapping techniques requires a refractive index mismatch between particles and solvent which leads to strong interparticle van der Waals interactions. Investigation of the behavior of systems without such strong attractive interactions, however, requires the uncoupling of particle refractive index and particle-particle interactions. To accomplish this, the synthesis of core-shell titania/silica particles has been performed. By index matching a silica shell on a titania core using a mixture of toluene and propanol, the van der Waals interactions between particles can be minimized. Due to the mismatch of the refractive index between the solvent and titania core, however, a strong trapping force can be generated, making optical manipulation feasible. In order to confirm that the silica shell was indeed matched, pure silica particles were synthesized by the method of St?ber (1968) and added to the core-shell system. In these mixed systems of core-shell and pure silica particles in silica-index-matching solvents, only the core-shell particles were trappable. Copyright 2000 Academic Press.     

van der Waals interactions of polycyclic aromatic hydrocarbon dimers

Density functional theory is in principle exact and includes also long-range interactions, such as the van der Waals interactions. These are, however, part of the exchange-correlation energy functional that needs to be approximated, and are absent in the local and semilocal standard implementations. Recently a density functional which includes van der Waals interactions for planar systems has been developed, which we show can be extended to provide a treatment of planar molecules. We use this functional to calculate binding distances and energies for dimers of three of the smallest polycyclic aromatic hydrocarbons (PAHs)--naphthalene, anthracene, and pyrene.     

Determination of van der Waals forces in monolayer films of lipids & biopolymers. Equation of state for two-dimensional films

Amphiphile molecules are characterized by the dual property arising from the interactions between the apolar [alkyl] and the polar part and the surrounding solvent, i.e., water. In assemblies which amphiphiles form in diverse systems, e.g., micelles, soap bubbles, monolayers or bilayers at interfaces, the attractive forces are attributed to the van der Waals forces. It is not easy to estimate the magnitude of van der Waals forces in some of these systems by any direct method.The magnitude of van der Waals forces in spread monolayers of lipids and biopolymers has been reported to be estimated from experimental data. The magnitude of these forces has been estimated by using an equation of state of a very general form, as delineated herein. In the current literature no such attempt has been reported in the analyses of these monolayers spread on aqueous surfaces. These analyses suggest that the predominant surface forces arise from van der Waals interactions, if the magnitude of electrostatic charge repulsions is weak. The equation-of-state as derived indicates that it is useful in providing information about the molecular interaction in monolayers, for both lipids and biopolymers.     

Stick slip contact mechanics between dissimilar materials: effect of charging and large friction

Measurements of the contact radius as a function of applied force between a mica surface and a silica surface (mica/silica) in air are reported. The load/unload results show that the contact radius generally increases with applied force. Because of the presence of charging due to contact electrification, both a short-range van der Waals adhesion force and longer-range electrostatic adhesive interaction contribute to the measured force. The results indicate that approximately 20% of the pull-off force is due to van der Waals forces. The contact radius versus applied force results can be fit to Johnson-Kendall-Roberts (JKR) theory by considering that only the short-range van der Waals forces contribute to the work of adhesion and subtracting a constant longer-range electrostatic force. Also, an additional and unexpected step function is superimposed on the contact radius versus applied force curve. Thus, the contact diameter increases in a stepped dependence with increasing force. The stepped contact behavior is seen only for increasing force and is not observed when symmetric mica/mica or silica/silica contacts are measured. In humid conditions, the contact diameter of the mica/silica contact increases monotonically with applied force. Friction forces between the surfaces are also measured and the shear stress of a mica/silica interface is 100 times greater than the shear stress of a mica/mica interface. This large shear stress retards the increase in contact area as the force is increased and leads to the observed stepped contact mechanics behavior.     

Wettability study of surface modified silica aerogels with different silylating agents

In wettability study, surface free energy interactions are of crucial importance for silica aerogels in which absorption of organic liquids and transportation of chemicals carried out for chemical and biotechnological applications. In present study, we have used Lifshitz–van der Waals/acid–base approach for calculation of surface free energy of aerogel sample. We have investigated that the surface free energy values of aerogels are 45.95, 51.42 and 45.69 mJ/m² by modifying their surfaces using 7 % chlorotrimethylsilane (TMCS), dimethyldichlorosilane (DMDCS) and hexamethyldisilazane (HMDZ) silylating reagents with solvent, respectively. The alcogels were prepared by two step acid–base catalyzed process where the molar ratio of precursors tetraethoxysilane:methanol:oxalic acid:NH₄OH:NH₄F was kept at optimal value of 1:16.5:0.71:0.58:0.60:0.98, respectively. To modify gel surfaces, TMCS, DMDCS and HMDZ concentration have been varied from 5 to 12 % and such alcogels were dried at ambient pressure. The aerogels have been characterized by fourier transform infrared spectroscopy, scanning electron microscopy, thermo-gravimetric and differential thermal analysis and Wetting properties of silica aerogel surfaces was studied by contact angle measurements. The surface chemical composition of DMDCS modified silica aerogels was studied by using X-ray photoelectron spectroscopy. As there is not any direct method, we have used Lifshitz–van der Waals/acid–base approach which gives, polar and non-polar components of aerogels surface free energy.     

Ionic liquid nanotribology: stiction suppression and surface induced shear thinning

The friction and adhesion between pairs of materials (silica, alumina, and polytetrafluoroethylene) have been studied and interpreted in terms of the long-ranged interactions present. In ambient laboratory air, the interactions are dominated by van der Waals attraction and strong adhesion leading to significant frictional forces. In the presence of the ionic liquid (IL) ethylammonium nitrate (EAN) the van der Waals interaction is suppressed and the attractive/adhesive interactions which lead to "stiction" are removed, resulting in an at least a 10-fold reduction in the friction force at large applied loads. The friction coefficient for each system was determined; coefficients obtained in air were significantly larger than those obtained in the presence of EAN (which ranged between 0.1 and 0.25), and variation in the friction coefficients between systems was correlated with changes in surface roughness. As the viscosity of ILs can be relatively high, which has implications for the lubricating properties, the hydrodynamic forces between the surfaces have therefore also been studied. The linear increase in repulsive force with speed, expected from hydrodynamic interactions, is clearly observed, and these forces further inhibit the potential for stiction. Remarkably, the viscosity extracted from the data is dramatically reduced compared to the bulk value, indicative of a surface ordering effect which significantly reduces viscous losses.     

Partitioning Solvophobic and Dispersion Forces in Alkyl and Perfluoroalkyl Cohesion

Fluorocarbons often have distinct miscibility properties compared to their nonfluorinated analogues. These differences may be attributed to van der Waals dispersion forces or solvophobic effects, but their contributions are notoriously difficult to separate in molecular recognition processes. Here, molecular torsion balances were used to compare cohesive alkyl and perfluoroalkyl interactions in a range of solvents. A simple linear regression enabled the energetic partitioning of solvophobic and van der Waals forces in the self‐association of apolar chains. The contributions of dispersion interactions in apolar cohesion were found to be strongly attenuated in solution compared to the gas phase, but still play a major role in fluorous and organic solvents. In contrast, solvophobic effects were found to be dominant in driving the association of apolar chains in aqueous solution. The results are expected to assist the computational modelling of van der Waals forces in solution.     

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.     

Van der waals interactions and decrease of the rotational barrier of methyl-sized rotators: a theoretical study

Rotational barriers of methyl-sized molecular rotators are investigated theoretically using ab initio and empirical force field calculations in molecular models simulating various environmental conditions experienced by the molecular rotors. Calculations on neopentane surrounded by methyl groups suggest that the neopentane's methyl rotational potential energy barrier can be reduced by up to an order of magnitude by locating satellite functional groups around the rotator at a geometry that destabilizes the staggered conformation of the rotator through van der Waals repulsive interactions and reduces the staggered/eclipsed relative energy difference. Molecular mechanics and molecular dynamics calculations indicate that this barrier-reducing geometry can also be found in molecular rotators surface mounted on graphite surfaces or carbon nanotube models. In these models, molecular dynamics simulations show that the rotation of methyl-sized functional groups can be catalyzed by van der Waals interactions, thus making very rigid rotators become thermally activated at room temperature. These results are discussed in the context of design of nanostructures and use of methyl groups as markers for microenvironmental conditions.     

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.     

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。     

Force measurements between Teflon AF and colloidal silica particles in electrolyte solutions

The interaction force between a very hydrophobic polymer surface and colloidal silica particles with a roughness of 10–15 nm has been measured in aqueous solutions of KOH and KCl using an atomic force microscope. The interaction can be described according to the DLVO theory by an electrical double-layer force that is repulsive at long distances and attractive at short distances and an attractive van der Waals force. The electrical double-layer potentials are compared to the zeta potentials of Teflon AF and the silica spheres. The roughness of the silica particles leads to an underestimation of the short-range attraction and the surface potential. Both KCl and KOH solutions affect the potential of the interacting surfaces. OH⁻ ions that adsorb preferentially to the Teflon AF surface create higher potentials than Cl⁻ ions. Range and strength of the attractive interaction are not affected by KCl solutions but reduced by addition of KOH. This can be explained by decreasing potential differences between the silica sphere and Teflon AF with increasing KOH concentration. In addition, the preferential adsorption of OH⁻ ions may lead to a reduction of the van der Waals interaction. The presence of nanobubbles, too, might play a role.     

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.     

The bridging force between two plates by polyelectrolyte chains

The interaction between particles in a colloidal system can be significantly affected by their bridging by polyelectrolyte chains. In this paper, the bridging is investigated by using a self-consistent field approach which takes into account the van der Waals interactions between the segments of the polyelectrolyte molecules and the plates, as well as the electrostatic and volume exclusion interactions. A positive contribution to the force between two plates is generated by the van der Waals interactions between the segments and the plates. This positive (repulsive) contribution plays an important role in the force when the distances between the plates are small. With increasing van der Waals interaction strength between segments and plates, the force between the plates becomes more repulsive at small distances and more attractive at large distances. When the surfaces of the plates have a constant surface electrical potential and a charge sign opposite to that of the polyelectrolyte chains, the force between the two plates becomes less attractive as the bulk polyelectrolyte concentration increases. This behavior is due to a higher bulk counterion concentration dissociated from the polyelectrolyte molecules. At short distances, the force between plates is more repulsive for stiffer chains. A comparison between theoretical and experimental results regarding the contraction of the interlayer separation between the platelets of vermiculite clays against the concentration of poly(vinyl methyl ether) was made.     

Structures and reaction mechanisms of cumene formation via benzene alkylation with propylene in a newly synthesized ITQ-24 zeolite: an embedded ONIOM study

The cumene formation via benzene alkylation with propylene on the new three-dimensional nanoporous catalyst, ITQ-24 zeolite, has been investigated by using the ONIOM2(B3LYP/6-31G(d,p):UFF) method. Both consecutive and associative reaction pathways are examined. The contributions of the short-range van der Waals interactions, which are explicitly included in the ONIOM2 model, and an additional long-range electrostatic potential from the extended zeolite framework to the energy profile are taken into consideration. It is found that benzene alkylation with propylene in the ITQ-24 zeolite prefers to occur through the consecutive reaction mechanism. The benzene alkylation step is the reaction rate-determining step with an estimated activation energy of 35.70 kcal/mol, comparable with an experimental report in beta-zeolite of 34.9 kcal/mol. The electrostatic potential from the extended zeolite framework shows a much more significant contribution to the transition state selectivity than the van der Waals interactions.