Peculiarities of long-range interaction between the nucleotides after DNA damage.

In this work, the long-range interaction between the pairs of nucleotides situated on the opposite ends of a double broken DNA helix have been studied theoretically. The long-range energy was considered as a sum of electrodynamics Van der Waals and electrostatic Coulomb interactions. The most important region for the problem under consideration is about 5-15 A between the nucleotides. The calculations of the energy of long-range interaction have shown that during the interaction between the pairs CG-CG, there is a potential repulsive barrier with the amplitude of about 4 kT at the distance of 7-9 A, and during the interaction between the pairs TA-TA, there is a potential repulsive barrier with the amplitude of about 1.5 kT at the same distance, which can prevent DNA from enzyme selfrepairing after a double DNA break. This barrier vanishes as the pH of intracellular medium increases. The remainder pairs of nucleotides do not have such barrier, and there is always an attraction like interaction.     

Interaction between a rodlike inclusion and a supported bilayer membrane

The interactions between a rodlike inclusion and a supported copolymer bilayer membrane are investigated by using the self-consistent field theory. For different system parameters, physical observables, such as the interaction free energy, entropy, and translocation energy barrier, are obtained. Particular emphasis is put on the closely energetic and entropic analyses of the interaction. It shows that the interfacial energy provides a qualitative trend and dominates the basic shape of the interaction free energy curve; the combination of chemical potential energy and total entropy contribution is responsible for the translocation energy barrier and the weak attraction in the vicinity of upper monolayer surface. We also specify the nature, height, and shape of the energy barrier to translocation. Particularly, the height is roughly proportional to the rod radius.     

Protein inclusion in lipid membranes: a theory based on the hypernetted chain integral equation

A theory for describing the structure of the hydrocarbon chains around a protein inclusion embedded in a lipid bilayer is developed on the basis of the hypernetted chain integral equation formalism for liquids. The exact lateral density-density response function of the hydrocarbon core, which is extracted from a molecular dynamics simulation of a pure lipid bilayer, is used as input to the theory. Numerical calculations show that the average lipid order is perturbed over a distance of 25 to 30 A around a hard repulsive cylinder of 5 A radius representing an alpha-helical polyleucine protein inclusion. The lipid-mediated protein-protein interaction is calculated and is shown to be non-monotonic, being repulsive at an intermediate range but attractive at short range. It is found that the lipid matrix contributes a free energy well of 8 kBT to the association of two cylindrical inclusions.     

Quantifying the anisotropy of intermolecular potential energy surfaces: a critical assessment of available N2-N2 potentials

Based on definition of angular central moments, a quantitative measure is proposed for comparative assessment of the anisotropy of different intermolecular potential energy surfaces at different intermolecular distances. Angular spreadness, skewness and peakedness are three features of anisotropy that are used here to describe the distribution of values of interaction energy around its isotropic component. In agreement with qualitative interpretations, the proposed measure exhibits a sharp change in the R-dependent pattern of anisotropy at an intermediate distance where the repulsive forces on the average overcome the attractive ones. The R-dependence of anisotropy of available N(2)-N(2) potentials is examined in comparison with bare ab initio data and considerable discrepancies are found at distances shorter than the onset of repulsion. It is shown that the full experimentally derived potentials with simplified functional forms do not reproduce the correct anisotropy of interaction energy.     

Interaction of nanometric clay platelets

The free energy of interaction between two nanometric clay platelets immersed in an electrolyte solution has been calculated using Monte Carlo simulations as well as direct integration of the configurational integral. Each platelet has been modeled as a collection of charged spheres carrying a unit charge the face of a platelet contains negative charges, and the edge, positive charges. The calculations predict that a configuration of "overlapping coins" is the global free energy minimum at intermediate salt concentrations (10-100 mM). A second weaker minimum, corresponding to the well-known "house of cards" configuration, also appears in this salt interval. At low salt concentrations the electrostatic repulsion dominates, while at intermediate concentrations electrostatic interactions alone can create a net attraction between the platelets. At sufficiently high salt content (>200 mM), the van der Waals interaction takes over and the net interaction becomes attractive at essentially all separations. From the calculated free energy and its derivative, we can derive a yield stress and elasticity modulus in fair agreement with experiment. The roughness of the platelets affects the quantitative behavior of the free energy of interaction but does not alter the results in a qualitative way. From the variation of the free energy of interaction, we would tentatively describe the phase behavior as follows: At low salt, the interaction is strongly repulsive and the dispersion should appear as a solid ("repulsive gel"). With increasing salt concentration, the repulsion is weakened and a liquid phase appears ("sol"). A further increase of the salt content leads a second solid phase ("attractive gel") governed by attractive interactions between the platelets. Finally, at sufficiently high salinity, the clay precipitates due to van der Waals forces.     

Electrical double-layer interaction between oppositely charged dissimilar oxide surfaces with charge regulation and Stern-Grahame layers

The force of double-layer interaction between dissimilar flat oxide surfaces charged oppositely at infinite separation and with Stern-Grahame layers was calculated as a function of the surface separation under the conditions of charge regulation. The interaction force showed a monotonic attraction with respect to the surface separation, lying between constant surface potential and constant surface charge conditions. The variations of surface potentials and surface charge densities of respective double layers were also presented as functions of the surface separation. When the negative diffuse-layer potential at infinite separation changed its sign to positive as a result of specific adsorption of cations on the negatively changed surface, the double-layer interaction force showed a repulsive force barrier followed by an attraction at some particular separation.     

The influence of solvation and finite temperatures on theWittig reaction: A theoretical study

The effects of the solvent and finite temperature (entropy) on the Wittig reaction are studied by using density functional theory in combination with molecular dynamics and a continuum solvation model. Standard gas-phase zero-temperature calculations are found to give similar results to previous studies. Gas-phase dynamics simulations allow the free energy profile of the reaction to be calculated through thermodynamic integration. The free energy profile is found to have a significant entropic barrier to the addition step of the reaction where only a small barrier was present in the potential energy curve. The introduction of the solvent dimethyl sulfoxide causes a change in the structure of the intermediate from the oxaphosphetane structure to the dipolar betaine structure. The overall reaction energy is changed only slightly. When the effects of both entropy and the solvent are included a significant entropic barrier to the addition reaction is obtained and the predicted intermediate again has the betaine structure.     

温度对二甲基亚砜水溶液的结构和热力学性质的影响

应用参考作用格位模型理论计算了二甲基亚砜(DMSO)摩尔分数为0.002时不同温度下溶液的微观结构和热力学性质. 计算结果表明, DMSO加入到水中能够增强溶液的分子网络结构. 温度升高, 配位数减小, 溶液中分子排布趋向无序. 平均力势的波动增大表明分子间的诱导力表现为斥力. 计算得到的各种热力学性质显示: 温度升高, 溶液的熵和溶剂化自由能增加, 相互作用能和过剩化学位也增加, 即高温下溶液越来越偏离理想溶液; 空位形成能降低表明溶液分子结构在高温下更容易重组.     

Comparative electrochemical scanning tunneling microscopy study of nonionic fluorosurfactant zonyl FSN self-assembled monolayers on Au(111) and Au(100): a potential-induced structural transition

We investigate the structure of nonionic fluorosurfactant zonyl FSN self-assembled monolayers on Au(111) and Au(100) in 0.05 M H(2)SO(4) as a function of the electrode potential by electrochemical scanning tunneling microscopy (ECSTM). On Au(111), a (3(1/2) × 3(1/2))R30° arrangement of the FSN SAMs is observed, which remains unchanged in the potential range where the redox reaction of FSN molecules does not occur. On Au(100), some parallel corrugations of the FSN SAMs are observed, which originate from the smaller distance and the repulsive interaction between FSN molecules to make the FSN molecules deviate from the bridging sites, and ECSTM reveals a potential-induced structural transition of the FSN SAMs. The experimental observations are rationalized by the effect of the intermolecular interaction. The smaller distance between molecules on Au(100) results in the repulsive force, which increases the probability of structural change induced by external factors (i.e., the electrode potential). The appropriate distance and interactions of FSN molecules account for the stable structure of FSN SAMs on Au(111). Surface crystallography may influence the intermolecular interaction through changing the molecular arrangements of the SAMs. The results benefit the molecular-scale understanding of the behavior of the FSN SAMs under electrochemical potential control.     

Compression induced chiral symmetry breaking of monolayers comprised of banana-shaped achiral molecules at an air-water interface: Williams-Bragg approach

Chirality of monolayers comprised of banana-shaped achiral molecules at an air-water interface was investigated theoretically, and a forming mechanism of chiral structure as an assembly of achiral molecules was argued. A model of such monolayers was constructed taking into account the short-range repulsive interaction between constituent banana-shaped achiral molecules, and the free energy density functional of the model was derived as a generalization of Williams-Bragg approach. It was predicted that chiral symmetry breaking occurs by monolayer compression, where two-dimensional characteristics of monolayers at an interface plays an important role in the formation of chiral structure by banana-shaped achiral molecules.     

Structure and stability of silica particle monolayers at horizontal and vertical octane-water interfaces

Monolayers of silica particles at horizontal and vertical octane-water interfaces have been studied by microscopy. It is found that their structure and stability depend strongly on the particle hydrophobicity. Very hydrophobic silica particles, with a contact angle of 152 degrees measured through the water, give well-ordered monolayers at interparticle distances larger than 5 particle diameters which are stable toward aggregation and sedimentation. In contrast, monolayers of less-hydrophobic particles are disordered and unstable. Two-dimensional particle sedimentation has been observed in the case of vertical monolayers. The results have been analyzed with a simple two-particle model considering the sedimentation equilibrium as a balance between the long-range electrostatic repulsion through the oil, the gravity force, and the capillary attraction due to deformation of the fluid interface around particles. The value of the charge density at the particle-octane interface, 14.1 muC/m(2), found for the most hydrophobic particles is reasonable. It drastically decreases for particles with lower hydrophobicity, which is consistent with the order-disorder transition in monolayer structure reported by us before. The pair interactions between particles at a horizontal octane-water interface have been analyzed including the capillary attraction due to undulated three-phase contact line caused by nonuniform wetting (the contact angle hysteresis). The results are in agreement with the great stability of very hydrophobic silica particle monolayers detected experimentally, even at low pH at the point of zero charge of the particle-water interface, and with the aggregated structure of hydrophilic particle monolayers.     

Internal and free energy in a pair of like-charged colloids: Monte Carlo simulations

The effective interaction between two colloidal particles in a bath of monovalent co- and counterions is studied by means of lattice Monte Carlo simulations with the primitive model. The internal electrostatic energy as a function of the colloid distance is studied fixing the position of the colloids. The free energy of the whole system is obtained introducing a bias parabolic potential, that allows us to sample efficiently small separations between the colloidal particles. For small charges, both the internal and free energy increase when the colloids approach each other, resulting in an effective repulsion driven by the electrostatic repulsion. When the colloidal charge is large enough, on the other hand, the colloid-ion coupling is strong enough to form double layers. The internal energy in this case decreases upon approaching the colloids because more ions enter the double layer. This attractive contribution to the interaction between the colloids is stronger for larger charges and larger ionic concentrations. However, the total free energy increases due to the loss of ionic entropy, and resulting finally in a repulsive interaction potential driven by the entropic contributions. The loss of ionic entropy can be almost quantitatively reproduced with the ideal contribution, the same level of approximation as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The overall behavior is captured by the DLVO theory qualitatively, and a comparison is made with the functional form predicted by the theory, showing moderate agreement.     

Coagulation of tobacco mosaic virus in alcohol-water-LiCl solutions

The coagulation and colloidal stability of tobacco mosaic virus (TMV) in alcohol-water-LiCl solutions were studied. Without the addition of LiCl salt, the coagulation was promoted by the increase of hydrophobicity of the alcohols that is proportional to their alkyl chain length and concentration. Addition of the LiCl salt reduced the electrostatic repulsion between TMV particles resulting in coagulation in methanol-water and ethanol-water solutions. In water-alcohol-LiCl mixture, the coagulation of TMV was driven by both the hydrophobic interaction of the solution and the screening effect of the salt simultaneously. To understand the particle-particle interaction during the coagulation, the interaction energy was calculated using DLVO theory. Considering the electrostatic repulsive energy, van der Waals attractive energy, and hydrophobic interaction energy, the total energy profiles were obtained. The experiment and model calculation results indicated that the increase of alcohol concentration would increase hydrophobic attraction energy so that the coagulation is promoted. These results provide the fundamental understanding on the coagulation of biomolecular macromolecules.     

Polymer-induced depletion interaction between weakly attractive plates

Lattice Monte Carlo simulations have been employed to calculate depletion interaction of excluded volume chains in a weakly attractive slit, particularly in the region around the critical point of adsorption. The simulations were performed under full equilibrium conditions where a dilute solution in a slit was in contact with the reservoir. The free energy of confinement deltaA, the force f, and the relative pressurepI/pE on the slit walls were calculated as a function of slit width D and the attraction strength epsilon. The depletion region in the pressure profile pI/pE vs D is reduced by an increase in the attraction potential epsilon in a manner resembling the influence of polymer concentration. At the critical point of adsorption epsilonc the depletion interaction vanishes both in the pressure pI/pE and in the intraslit concentration profile phiI(x). The parameters used to assess the stability of colloidal dispersions such as the depletion potential W(D) (an integral of the net pressure deltap) reach a unique value at the critical condition. A monotonic repulsive profilepI vs D was found for chains trapped in the slit at restricted equilibrium. The mean dimensions (R2) of chains compressed in attractive slits feature a distinct minimum at intermediate slit widths.     

The role of hydrophobic surfaces in altering water-mediated peptide-peptide interactions in an aqueous environment

Using Born-Oppenheimer molecular dynamics within the density functional framework, we calculated the effective force acting on water-mediated peptide-peptide interaction between antiparallel β-sheets in an aqueous environment and also in the vicinity of a hydrophobic surface. From the magnitude of the effective force (corresponding to the slope of the free energy as a function of the interpeptide distance) and its sign (a negative value indicates an effective attraction, whereas a positive value indicates an effective repulsion) we can elucidate the fundamental differences of the water-mediated peptide-peptide interactions in those two environments. The computed effective forces indicate that the water-mediated interaction between peptides in an aqueous environment is attractive in the range of interpeptide distance d = 7-8 ? when hydrophobic surfaces are not nearby. Due to the stabilization of the water molecules bridging between the two β-sheets, a free energy barrier exists between the direct and indirect (water-mediated) interpeptide interactions. However, when the peptides are in the proximity of hydrophobic surfaces, this free energy barrier decreases because the hydrophobic surfaces enhance the interpeptide attraction by the destabilization and ease-to-libration of the bridging water molecules between them.     

Negative electron affinities from conventional electronic structure methods

If the potential V describing the interaction between an excess electron and a ground-state neutral or anionic parent is sufficiently attractive at short range, electron-attached states having positive electron affinities (EAs) can arise. Even if the potential is not attractive enough to produce a bound state, metastable electron-attached states may still occur and have lifetimes long enough to give rise to experimentally detectable signatures. Low-energy metastable states arise when the attractive components of V combine with a longer-range repulsive contribution to produce a barrier behind which the excess electron can be temporarily trapped. These repulsive contributions arise from either the centrifugal potential in the excess electron’s angular kinetic energy or long-range Coulomb repulsion in the case of an anionic parent. When there is no barrier, this kind of low-energy metastable state does not arise, but improper theoretical calculations can lead to erroneous predictions of their existence. Conventional electronic structure methods with, at most, minor modifications are described for properly characterizing metastable states and for avoiding incorrectly predicting the existence of metastable states with negative EAs where no barrier is present.     

The interaction between colloids in polar mixtures above Tc

We calculate the interaction potential between two charged colloids immersed in an aqueous mixture containing salt near or above the critical temperature. We find an attractive interaction far from the coexistence curve due to the combination of preferential solvent adsorption at the colloids' surface and preferential ion solvation. We show that the ion-specific interaction strongly depends on the amount of salt added as well as on the mixture composition. The calculations are in good agreement with recent experiments. For a highly antagonistic salt of hydrophilic anions and hydrophobic cations, a repulsive interaction at an intermediate inter-colloid distance is predicted even though both the electrostatic and adsorption forces alone are attractive.     

Molecular simulations of surface forces and film rupture in oil/water/surfactant systems

We use dissipative particle dynamics (DPD) and molecular models to simulate interacting oil/water/surfactant interfaces. The system comprises sections of two emulsion droplets separated by a film. The film is in equilibrium with a continuous phase, in analogy with the surface force apparatus. This is achieved by combining DPD with a Monte Carlo scheme to simulate a muVT ensemble. The setup enables the computation of surface forces as a function of the distance between the two interfaces, as well as the detection of film rupture. We studied monolayers of nonionic model surfactants at different densities and compared oil-water-oil and water-oil-water emulsion films. Between surfactant monolayers facing each other tails-on (water-oil-water films), we observed repulsive forces due to the steric interaction between overlapping hydrophobic tails. The repulsion increases with surfactant density. Conversely, no such repulsion is observed between surfactant monolayers facing each other heads-on. Instead, the film ruptures, the monolayers merge, and a channel forms between the two droplet phases. Film rupture can also be induced in the water-oil-water films by forcing the interfaces together. The separation at rupture increases for oil-water-oil films and decreases for water-oil-water films when the surfactant density increases. The results are in qualitative agreement with existing theories of emulsion stability in creams, in particular with the channel nucleation theory based on the natural curvature of surfactants.     

Haloing, flocculation, and bridging in colloid-nanoparticle suspensions

Integral equation theory with a hybrid closure approximation is employed to study the equilibrium structure of highly size asymmetric mixtures of spherical colloids and nanoparticles. Nonequilibrium contact aggregation and bridging gel formation is also qualitatively discussed. The effect of size asymmetry, nanoparticle volume fraction and charge, and the spatial range, strength, and functional form of colloid-nanoparticle and colloid-colloid attractions in determining the potential-of-mean force (PMF) between the large spheres is systematically explored. For hard, neutral particles with weak colloid-nanoparticle attraction qualitatively distinct forms of the PMF are predicted: (i) a contact depletion attraction, (ii) a repulsive form associated with thermodynamically stable "nanoparticle haloing," and (iii) repulsive at contact but with a strong and tight bridging minimum. As the interfacial cohesion strengthens and becomes shorter range the PMF acquires a deep and tight bridging minimum. At sufficiently high nanoparticle volume fractions, a repulsive barrier then emerges which can provide kinetic stabilization. The charging of nanoparticles can greatly reduce the volume fractions where significant changes of the PMF occur. For direct and interfacial van der Waals attractions, the large qualitative consequences of changing the absolute magnitude of nanoparticle and colloid diameters at fixed size asymmetry ratio are also studied. The theoretical results are compared with recent experimental and simulation studies. Calculations of the real and Fourier space mixture structure at nonzero colloid volume fractions reveal complex spatial reorganization of the nanoparticles due to many body correlations.