Tuning the dynamics and molecular distribution of the self-spreading lipid bilayer

The self-spreading dynamics of lipid bilayers were investigated at controlled electrolyte concentrations. The self-spreading velocity increased when the concentration of NaCl was increased from 1 to 100 mM. Comparing the experimentally determined spreading energy with that estimated from theoretical models, we found that the self-spreading dynamics were well explained by considering the van der Waals interaction, double layer interaction and hydration interaction energies between the self-spreading bilayer and the substrate. The characteristic behavior at high concentration is attributable to the increase in the density of the lipid layer, originating from the effective shielding of the molecular charges by the electrolyte ions in solution. The distribution of doped dye-labeled molecule within the spreading bilayer was also controllable by tuning the electrolyte concentration. All of these findings were explained by systematic changes in bilayer-substrate or inter-molecular interactions depending on the electrolyte concentration.     

Can Dispersion Forces Govern Aromatic Stacking in an Organic Solvent?

Experimental support for the dominance of van der Waals dispersion forces in aromatic stacking interactions occurring in organic solution is surprisingly limited. The size‐dependence of aromatic stacking in an organic solvent was examined. The interaction energy was found to vary by about 7.5 kJ mol^?1 on going from a phenyl–phenyl to an anthracene–pyrene stack. Strikingly, the experimental data were highly correlated with dispersion energies determined using symmetry‐adapted perturbation theory (SAPT), while the induction, exchange, electrostatic, and solvation energy components correlated poorly. Both the experimental data and the SAPT‐dispersion energies gave high‐quality correlations with the change in solvent accessible area upon complexation. Thus, the size‐dependence of aromatic stacking interactions is consistent with the dominance of van der Waals dispersion forces even in the presence of a competing polarizable solvent.     

Can Dispersion Forces Govern Aromatic Stacking in an Organic Solvent?

Experimental support for the dominance of van der Waals dispersion forces in aromatic stacking interactions occurring in organic solution is surprisingly limited. The size‐dependence of aromatic stacking in an organic solvent was examined. The interaction energy was found to vary by about 7.5 kJ mol⁻¹ on going from a phenyl–phenyl to an anthracene–pyrene stack. Strikingly, the experimental data were highly correlated with dispersion energies determined using symmetry‐adapted perturbation theory (SAPT), while the induction, exchange, electrostatic, and solvation energy components correlated poorly. Both the experimental data and the SAPT‐dispersion energies gave high‐quality correlations with the change in solvent accessible area upon complexation. Thus, the size‐dependence of aromatic stacking interactions is consistent with the dominance of van der Waals dispersion forces even in the presence of a competing polarizable solvent.     

Electrostatic control of lipid bilayer self-spreading using a nanogap gate on a solid support

We have demonstrated for the first time that the self-spreading of supported lipid bilayers can be controlled by the temporal switching of an electric field applied between nanogap electrodes. To account for this phenomenon, we propose an electrostatic trapping model in which an electric double layer plays an important role. The validity of this mechanism was verified by the dependence of self-spreading on the nanogap width and the ionic concentration of the electrolyte. Our results provide a promising tool for the temporal and spatial control of lipid bilayer formation for nanobio devices.     

Revealing the Preferred Interlayer Orientations and Stackings of Two‐Dimensional Bilayer Gallium Selenide Crystals

Characterizing and controlling the interlayer orientations and stacking orders of two‐dimensional (2D) bilayer crystals and van der Waals (vdW) heterostructures is crucial to optimize their electrical and optoelectronic properties. The four polymorphs of layered gallium selenide (GaSe) crystals that result from different layer stackings provide an ideal platform to study the stacking configurations in 2D bilayer crystals. Through a controllable vapor‐phase deposition method, bilayer GaSe crystals were selectively grown and their two preferred 0° or 60° interlayer rotations were investigated. The commensurate stacking configurations (AA′ and AB stacking) in as‐grown bilayer GaSe crystals are clearly observed at the atomic scale, and the Ga‐terminated edge structure was identified using scanning transmission electron microscopy. Theoretical analysis reveals that the energies of the interlayer coupling are responsible for the preferred orientations among the bilayer GaSe crystals.     

^1^7O, ^3^3S NMR化学位移结构效应的分子力学研究

本文通过对环状磷酸酯和环状亚磷酸酯类化合物的分子力学计算,观察到^1^7ONMR化学位移的变化同时受到氧原子局部范德华相互综合利用(E~V~D~W~-~O)和局部偶极相互作用能(E~i~i~p-~O)的影响。此外,在上述两类化合物中,环外氧原子的δ-压缩效应极为明显,这主要是由于该氧原子局部范德华相互作用能起决定作用的缘故。同时,经对二烷基砜类化合物的分子力学计算,首次获得^3^3SNMR化学位移和硫原子局部范德华相互作用能E~V~D~W~-~S之间良好的线性关系。     

Microchannel device using self-spreading lipid bilayer as molecule carrier

We propose a microchannel device that employs a surface-supported self-spreading lipid bilayer membrane as a molecule carrying medium. The device has a micropattern structure fabricated on a SiO2 surface by photolithography, into which a self-spreading lipid bilayer membrane is introduced as the carrier medium. This system corresponds to a microchannel with a single lipid bilayer membrane height of approximately 5 nm, compared with conventional micro-fluidic channels that have a section height and width of at least several microm. The device is beneficial for detecting intermolecular interactions when molecules carried by the self-spreading lipid bilayer collide with each other in the microchannel. The validity of the device was confirmed by observing the fluorescence resonance energy transfer (FRET) between two dye molecules, coumarin and fluorescein.     

糖和盐类物质对生物膜超分子结构稳定性影响的研究

用原子力显微镜(AFM)和小角X射线(SAXS)技术, 研究了NaCl、KCl、胆固醇、葡萄糖和蔗糖等与膜脂的相互作用. 研究发现它们能引起脂质膜超分子体系液晶态结构的变化. 葡萄糖和蔗糖对脂双层膜结构有稳定作用. 在NaCl溶液中制成的脂质膜, 随着NaCl浓度的增加, 它们的双层膜更稳定. 在KCl溶液中结果恰好相反. AFM研究发现液晶态脂双层膜结构与双亲性分子的结构、浓度以及介质的组分和pH等因素有关. 在1,2-反十八碳-3-磷脂酰乙醇胺(DEPE)液晶态中, 钠盐诱导形成Q²²⁹(Im3m)立方相. 油酸的含量对DEPE-PVP(聚乙烯吡咯烷酮)超分子结构也有一定的影响, 当油酸含量达到某一临界值时, 则发生从Im3m(Q²²⁹)到Pn3m(Q²²⁴)的转变. 胆固醇能促使形成Pn3m(Q²²⁴)和六角相H_II共存相. 研究结果表明, 生物膜超分子聚集体的氢键、分子van der Waals力、离子的静电力等这些弱相互作用的协同性、方向性和选择性, 可能决定着生物膜的结构和功能.     

Adsorption of ions onto polymer surfaces and its influence on zeta potential and adhesion phenomena

 The adhesion behavior that governs many technologically and biologically relevant polymer properties can be investigated by zeta potential measurements with varied electrolyte concentration or pH. In a previous work [1] it was found that the difference of the adsorption free energies of Cl^- and K⁺ ions correlates with the adhesion force caused by van der Waals interactions, and that the decrease of adhesion strength by adsorption layers can be elucidated by zeta potential measurements. In order to confirm these interrelations, zeta potential measurements were combined with atomic force microscopy (AFM) measurements. Force–distance curves between poly(ether ether ketone) and fluorpolymers, respectively, and the Si₃N₄ tip of the AFM device in different electrolyte solutions were measured and analysed. The adsorption free energy of anions calculated from the Stern model correlates with their ability to prevent the adhesion between the polymer surface and the Si₃N₄ tip of the AFM device. These results demonstrate the influence of adsorption phenomena on the adhesion behavior of solids. The results obtained by AFM confirm the thesis that the electrical double layer of solid polymers in electrolyte solutions is governed by ion adsorption probably due to van der Waals interactions and that therefore van der Waals forces can be detected by zeta potential measurements. Received: 18 November 1997 Accepted: 19 January 1998     

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy

Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling of conformational equilibria. The nonpolar component of the hydration free energy, consisting of a repulsive cavity term and an attractive van der Waals solute-solvent interaction term, is often modeled using estimators based on the solvent exposed solute surface area. In this paper, we analyze the accuracy of linear surface area models for predicting the van der Waals solute-solvent interaction energies of native and non-native protein conformations, peptides and small molecules, and the desolvation penalty of protein-protein and protein-ligand binding complexes. The target values are obtained from explicit solvent simulations and from a continuum solvent van der Waals interaction energy model. The results indicate that the standard surface area model, while useful on a coarse-grained scale, may not be accurate or transferable enough for high resolution modeling studies of protein folding and binding. The continuum model constructed in the course of this study provides one path for the development of a computationally efficient implicit solvent nonpolar hydration free energy estimator suitable for high-resolution structural and thermodynamic modeling of biological macromolecules.     

Communication: Length scale dependent oil-water energy fluctuations

Interfacial fluctuations in the cohesive (van der Waals) interaction energy of spherical oil-drops with water provide evidence of a length scale dependent transition from linear to non-linear response behavior. For sub-nanometer oil-drop sizes, energy fluctuations are found to be independent of the van der Waals coupling strength, while nanometer (and larger) size oil drops experience highly non-linear energy fluctuations. The latter behavior is linked to enhanced hydrophobic density fluctuations and the emergence of entropic contributions to oil-water cohesive interaction free energies.     

Van der Waals interactions: evaluations by use of a statistical mechanical method

In this work the induced van der Waals interaction between a pair of neutral atoms or molecules is considered by use of a statistical mechanical method. With use of the Schro?dinger equation this interaction can be obtained by standard quantum mechanical perturbation theory to second order. However, the latter is restricted to electrostatic interactions between dipole moments. So with radiating dipole-dipole interaction where retardation effects are important for large separations of the particles, other methods are needed, and the resulting induced interaction is the Casimir-Polder interaction usually obtained by field theory. It can also be evaluated, however, by a statistical mechanical method that utilizes the path integral representation. We here show explicitly by use of this method the equivalence of the Casimir-Polder interaction and the van der Waals interaction based upon the Schro?dinger equation. The equivalence is to leading order for short separations where retardation effects can be neglected. In recent works [J. S. H?ye, Physica A 389, 1380 (2010); Phys. Rev. E 81, 061114 (2010)], the Casimir-Polder or Casimir energy was added as a correction to calculations of systems like the electron clouds of molecules. The equivalence to van der Waals interactions indicates that the added Casimir energy will improve the accuracy of calculated molecular energies. Thus, we give numerical estimates of this energy including analysis and estimates for the uniform electron gas.     

锕系配合物中Vander Waals能与配位键能之间的平衡I:

对铀的几个络合物的配位键和Van der Waals能之间的平衡进行分析研究,发现在配位原子间配合键能和最大Van der Waals引力能几乎一致,这有力地支持了堆积模型将成为这一模型进一步发展的基础.     

On the interdependence of van der waals and double layer forces

We study the effect of coupling the electrostatic and low frequency electrodynamic responses of colloidal systems. Exact results are reported for the van der Waals free energy of interaction of non-uniform electrolyte across planar dielectric and planar charged dielectric across non-uniform electrolyte. In both cases, the results depend on the double layer repulsion.     

Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes

A new computational approach to calculating binding energies and spatial positions of small molecules, peptides, and proteins in the lipid bilayer has been developed. The method combines an anisotropic solvent representation of the lipid bilayer and universal solvation model, which predicts transfer energies of molecules from water to an arbitrary medium with defined polarity properties. The universal solvation model accounts for hydrophobic, van der Waals, hydrogen-bonding, and electrostatic solute-solvent interactions. The lipid bilayer is represented as a fluid anisotropic environment described by profiles of dielectric constant (ε), solvatochromic dipolarity parameter (π*), and hydrogen bonding acidity and basicity parameters (α and β). The polarity profiles were calculated using published distributions of quasi-molecular segments of lipids determined by neutron and X-ray scattering for DOPC bilayer and spin-labeling data that define concentration of water in the lipid acyl chain region. The model also accounts for the preferential solvation of charges and polar groups by water and includes the effect of the hydrophobic mismatch for transmembrane proteins. The method was tested on calculations of binding energies and preferential positions in membranes for small-molecules, peptides and peripheral membrane proteins that have been experimentally studied. The new theoretical approach was implemented in a new version (2.0) of our PPM program and applied for the large-scale calculations of spatial positions in membranes of more than 1000 peripheral and integral proteins. The results of calculations are deposited in the updated OPM database ( http://opm.phar.umich.edu ).     

Pancake Bond Orders of a Series of π‐Stacked Triangulene Radicals

Conjugated radicals are capable of forming π‐stacking “pancake‐bonded” dimers. Members of the family of triangulene hydrocarbons, non‐Kekulé neutral multiradicals, can utilize more than one singly occupied molecular orbital (SOMO) to form multiple pancake‐bonded dimers with formal bond orders of up to five. The resulting dimer binding energies can be quite high and the intermolecular contacts rather small compared to the respective van der Waals values. The preferred configurations are driven by the large stabilization energy of overlapping SOMOs.     

Donor–Acceptor Mechanism of Complex Formation

The gas-phase van der Waals complexes formed in the course of donor–acceptor interaction are shown to become coordination compounds only in the crystalline state. With close lengths of the covalent-ionic and coordination bonds, their energies differ by 100 kJ. This energy difference is due to the work spent to overcome van der Waals forces during the formation of complex ions from interacting molecules.     

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.     

Effects of lipid chain length on molecular interactions between paclitaxel and phospholipid within model biomembranes

Molecular interactions between an anticancer drug, paclitaxel, and phosphatidylcholine (PC) of various chain lengths were investigated in the present work by the Langmuir film balance technique and differential scanning calorimetry (DSC). Both the lipid monolayer at the air-water interface and lipid bilayer vesicles (liposomes) were employed as model biological cell membranes. Measurement and analysis of the surface pressure versus molecular area curves of the mixed monolayers of phospholipids and paclitaxel under various molar ratio showed that phospholipids and paclitaxel formed a nonideal miscible system at the interface. Paclitaxel exerted an area-condensing effect on the lipid monolayer at small molecular surface areas and an area-expanding effect at large molecular areas, which could be explained by the intermolecular forces and geometric accommodation between the two components. Paclitaxel and phospholipids could form thermodynamically stable monolayer systems: the stability increased with the chain length in the order DMPC (C14:0)>DPPC (C16:0)>DSPC (C18:0). Investigation of paclitaxel penetration into the pure lipid monolayer showed that DMPC had a higher ability to incorporate paclitaxel and the critical surface pressure for paclitaxel penetration also increased with the chain length in the order DMPC>DPPC>DSPC. A similar trend was testified by DSC studies on vesicles of the mixed paclitaxel/phospholipids bilayer. Paclitaxel showed the greatest interaction with DMPC while little interaction could be measured in the paclitaxel/DSPC liposomes. Paclitaxel caused broadening of the main phase transition without significant change at the peak melting temperature of the phospholipid bilayers, which demonstrated that paclitaxel was localized in the outer hydrophobic cooperative zone of the bilayer. The interaction between paclitaxel and phospholipid was nonspecific and the dominant factor in this interaction was the van der Waals force or hydrophobic force. As the result of the lower net van der Waals interaction between hydrocarbon chains for the shorter acyl chains, paclitaxel interacted more readily with phospholipids of shorter chain length, which also increased the bilayer intermolecular spacing.     

Stacking of Exfoliated Two‐Dimensional Materials: A Review

In recent years, two‐dimensional (2D) atomic crystals represented by graphene have opened up new fields of 2D physics. Layered materials with atomic layer thickness are self‐assembled into van der Waals heterostructures by weak van der Waals forces without considering lattice matching. Van der Waals heterostructures can not only enhance the performance of its constituent materials but also show new characteristics. High‐quality heterostructures require mechanically cleaved intrinsic 2D materials and flexible 2D material stacking techniques. Here, we summarize in detail the reliable exfoliation methods for large‐area single‐layer 2D materials and the dry and wet stacking techniques with high success rates. The twisted bilayer graphene is used as an example to briefly introduce the single‐crystal tearing method, which is currently the most practical method for preparing isotropic twisted heterostructures with high‐precision rotation angles. We hope to provide a valuable reference for researchers of 2D materials.