The Structure of Cellulose by Conformational Analysis. 1. Cellobiose and Methyl-β-cellobioside

Conformational analysis studies on the tertiary structure of cellobiose and methyl-β-cellobioside were carried out by using calculations of van der Waals, H-bond, electrostatic, and torsional energy interactions between the atoms and groups of the molecules. Energy maps as functions of the rotational anglesΨo and Φ° of the glucosidic bond were obtained in increments of 20° and refined in increments of 1°. Two “primary” and one “secondary” conformations of minimum energy were obtained for both cellobiose and methyl-β-cellobioside, some of which are equivalent to results obtained by x-ray diffraction. The H-bond forces are shown to be, together with the van der Waals forces, the predominant factors in the fixation of the conformations of minimum energy. The position and energy contributions of the H-bonds patterns for the favored conformations are identified.     

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.     

EGFR和4-苯胺喹唑啉类抑制剂之间相互作用模式的研究

采用分子动力学和MM/PBSA相结合的方法预测了表皮生长因子受体和4-苯胺喹 啉类抑制剂的相互作用模式。在分子动力学采样的基础上,采用MM/PBSA的方法分 别预测了四种可能结合模式下表皮生长因子受体和4-苯胺喹唑啉类抑制剂间的结合 自由能。在MM/PBSA计算中,受体和抑制剂之间的非键相互作用能采用分子力学 (MM)的方法得到;溶剂效应中极性部分对自由能的贡献通过解Possion- Boltzmanne (PB)方程的方法得到;溶液效应中非极性部分对自由能的贡献则通过 分子表面积计算(SA)的方法得到。计算表明,在四种结合模式下,表皮生长因子受 体和4-苯胺喹唑啉类抑制剂之间的结合自由能有较大的差别。在最佳的相互作用模 式中,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。抑制剂喹唑啉环上的N(1)原子能够和Met-769上的 NH形成稳定的氢键,而抑制剂上的N(3)原子则和周围的一个水分子形成氢键。同时 ,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 水相互作用。最佳结合模式能够很好地解释已有抑制剂结构和活性间的关系。     

The Structure of Cellulose by Conformational Analysis. Part 4. Crystalline Cellulose II

The Kolpack, Weih, and Blackwell antiparallel central chain model was found to be the most energetically stable for the crystalline structure of cellulose II. Computational results indicated that the two most probable Sarko models are considerably less stable and less probable. The conformations of the monomers terminating the crystalline zone have been described. The predominance of van der Waals and H-bond interactions in the crystalline zone have been confirmed, and the H-bond values, locations, and distribution in the crystalline zone have been accurately mapped. The cellulose II crystallite has been confirmed to be considerably more stable than the cellulose I crystallite. Positions of atomic groups from the ab initio conformational analysis are consistent with the x-ray data for the Kolpack, Weih, and Blackwell model.     

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.     

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.     

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.     

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.     

Calculation of alcohol conformations by molecular mechanics

The geometries and energies of simple alcohols were calculated with a molecular mechanics force field. The force field requires the application of the charge interaction model with charges calculated by the CNDO/2 method, the importance of electrostatic interactions for the equilibrium of rotamers about the C-O bond exceeds that of van der Waals interactions. The calculated rotamer populations are discussed with regard to the value of ¹H NMR coupling constants ³JHCOH and other experimental data.     

Interaction Forces between Hydrophobic and Hydrophilic Self-Assembled Monolayers

An investigation is presented of the interaction of charged self-assembled monolayers (SAMs) with a monoprotic ionizable acid functional group (-COOH) and uncharged SAMs with a methyl terminated functional group (-CH(3)). The strength of the interactions are determined using an atomic force microscope. For all electrolyte conditions investigated the interactions are not well described by a summation of van der Waals attractions and electrostatic repulsions in a manner suggesting that van der Waals attractions are screened. The repulsions are accurately described as corresponding to two surfaces of different charge interacting with surface charges that are independent of separation (i.e., the constant charge model). A small adhesion force was observed under all conditions and its magnitude increased with NaCl concentration. Copyright 2000 Academic Press.     

Wetting behavior of pentane on water. The analysis of temperature dependence

The temperature dependence of wetting behavior for pentane on water is analyzed from the standpoint of the Derjaguin-Frumkin theory. The joint action of two mechanisms of surface forces, the van der Waals and the image charge interactions, are considered to calculate the isotherms of the disjoining pressure. To analyze the temperature influence on the magnitude of van der Waals forces, we have used the exact Dzyaloshinsky, Lifshitz, and Pitaevsky equation. It is shown that image forces, arising due to the restricted solubility of water in pentane, decay much faster with increasing the film thickness and can be considered as short ranged in comparison to the van der Waals forces. The competitive action of the image charge and the van der Waals forces provides the plausible explanation of the temperature dependence of wetting in the system under consideration.     

Ionic Liquids: Dissecting the Enthalpies of Vaporization

We calculate the heats of vaporisation for imidazolium‐based ionic liquids [C_nmim][NTf₂] with n=1, 2, 4, 6, 8 by means of molecular dynamics (MD) simulations and discuss their behavior with respect to temperature and the alkyl chain length. We use a force field developed recently. The different cohesive energies contributing to the overall heats of vaporisations are discussed in detail. With increasing alkyl chain length, the Coulomb contribution to the heat of vaporisation remains constant at around 80 kJ mol^?1, whereas the van der Waals interaction increases continuously. The calculated increase of about 4.7 kJ mol^?1 per CH₂‐group of the van der Waals contribution in the ionic liquid exactly coincides with the increase in the heats of vaporisation for n‐alcohols and n‐alkanes, respectively. The results support the importance of van der Waals interactions even in systems completely composed of ions.     

van der Waals interaction between internal aqueous droplets and the external aqueous phase in double emulsions

A mathematical model for analyzing the van der Waals interaction between the internal aqueous droplets (W(1)) and the external aqueous phase (W(2)) of double emulsions has been established. The effects of Hamaker constants of the materials forming the system, especially those of the two different adsorbed surfactant layers with uniform density (A(1) and A(2)), on the van der Waals interaction were investigated. The overall van der Waals interaction across the oil film is a combined result of four individual parts, that is, W(1)-W(2), A(1)-A(2), W(1)-A(1), and A(2)-W(2) van der Waals interaction, and it may be either attractive or repulsive depending on many factors. It was found that the overall van der Waals interaction is dominated by the W(1)-W(2) interaction at large separation distances between the W(1)/O and O/W(2) interfaces, while it is mostly determined by the A(1)-A(2) interaction when the two interfaces are extremely close. Specifically, in the cases when the value of the Hamaker constant of the oil phase is intermediate between those of W(1) and W(2) and there is a thick oil film separating the two interfaces, a weak repulsive overall van der Waals interaction will prevail. If the Hamaker constant of the oil phase is intermediate between those of A(1) and A(2) and the two interfaces are very close, the overall van der Waals interaction will be dominated by the strong repulsive A(1)-A(2) interaction. The repulsive van der Waals interaction at such cases helps stabilize the double emulsions.     

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.     

Retention vs van der walls volume,pi-energy and hydrogen-bonding energy effects and enthalpy in liquid chromatography

Summary The logarithm of capacity ratios (logk’) of alkanes, alkyl alcohols, alkylbenzenes, halogenated benzenes and polyaromatic hydrocarbons are measured in reversedphase liquid chromatography at several temperatures using an octadecyl-bonded silica gel as the packing and acetonitrile/water mixtures as the eluent. The Δ (logk’) values are related to their van der Waals volumes, pi-energy and hydrogen-bonding energy effects and their enthalpies. The difference between the observed capacity ratios and the capacity ratios predicted from van der Waals volumes, pi-energy and hydrogen-bonding energy effects can be explained due to enthalpy effect of larger molecular size compounds. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

Studies on the interaction mechanism between CXS and papain by spectroscopic and molecular modeling methods

We have studied the interaction between cefuroxime sodium (CXS) and papain at different temperatures by a fluorescence method, and confirmed that the mechanism of fluorescence quenching of CXS to papain is mainly static quenching. We also determined the binding constant K. Based on the thermodynamic functions at different temperatures, the results show that the major forces between CXS and papain are van der Waals’ forces and H bond. According to the Forster non-radiation energy transfer mechanism, we determined the binding distance between CXS and papain, and studied the confirmation effect of CXS to papain by synchronous fluorescence and UV–Vis spectroscopy. Molecular simulations show that the binding types of CXS and papain are van der Waals’ forces, hydrophobic interaction, and H-bond.     

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.     

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。     

Trajectory Analysis and Collision Efficiency during Microbubble Flotation

The hydrodynamic interaction between a rising bubble and a sedimenting particle during microbubble flotation is considered. The effects of attractive van der Waals forces and attractive or repulsive electrostatic forces are included. A mathematical model is presented which is used to perform a trajectory analysis and to calculate collision efficiencies between the bubble and particle. It is shown that collision efficiencies and the nature of the bubble-particle interactions are strongly dependent on the relative strengths of the van der Waals and electrostatic forces and on the lengthscales over which these forces act. It is demonstrated that optimal operating conditions can be suggested to achieve efficient microbubble flotation by correctly accounting for the interaction of van der Waals, electrostatic, and hydrodynamic forces. Copyright 1999 Academic Press.