Effect of solute size and solute-water attractive interactions on hydration water structure around hydrophobic solutes.

Using Monte Carlo simulations, we investigated the influence of solute size and solute-water attractive interactions on hydration water structure around spherical clusters of 1, 13, 57, 135, and 305 hexagonally close-packed methanes and the single hard-sphere (HS) solute analogues of these clusters. We obtain quantitative results on the density of water molecules in contact with the HS solutes as a function of solute size for HS radii between 3.25 and 16.45 A. Analysis of these results based on scaled-particle theory yields a hydration free energy/surface area coefficient equal to 139 cal/(mol A2), independent of solute size, when this coefficient is defined with respect to the van der Waals surface of the solute. The same coefficient defined with respect to the solvent-accessible surface decreases with decreasing solute size for HS radii less than approximately 10 A. We also find that solute-water attractive interactions play an important role in the hydration of the methane clusters. Water densities in the first hydration shell of the three largest clusters are greater than bulk water density and are insensitive to the cluster size. In contrast, contact water densities for the HS analogues of these clusters decrease with solute size, falling below the bulk density of water for the two largest solutes. Thus, the large HS solutes dewet, while methane clusters of the same size do not.     

Cluster expansion of electronic excitations: application to fcc Ni-Al alloys

The cluster expansion method is applied to electronic excitations and a set of effective cluster densities of states (ECDOS) is defined, analogous to effective cluster interactions (ECIs). The ECDOSs are used to generate alloy thermodynamic properties as well as the equation of state (EOS) of electronic excitations for the fcc Ni-Al systems. When parent clusters have a small size, the convergence of the expansion is not so good but the electronic density of state (DOS) is well reproduced. However, the integrals of the DOS such as the cluster expanded free energy, entropy, and internal energy associated with electronic excitations are well described at the level of the tetrahedron-octahedron cluster approximation, indicating that the ECDOS is applicable to produce electronic ECIs for cluster variation method (CVM) or Monte Carlo calculations. On the other hand, the Gruneisen parameter, calculated with first-principles methods, is no longer a constant and implies that the whole DOS profile should be considered for EOS of electronic excitations, where ECDOS adapts very well for disordered alloys and solid solutions.     

Helix formation in the polymer brush

This work considers the physics of a brush formed by polymers capable of undergoing a helix-coil transition. A self-consistent field approximation for strongly stretched polymer chains is used in combination with a lattice model of the interaction energy in helix-coil mixtures. Crowding-induced chain stretching stabilizes helix formation at moderate tethering densities while high tethering density causes sufficiently strong stretching to unravel segments of the helix, resulting in distinct layers of monomer density and helical content. Compared to a random-coil brush at low-to-moderate tethering density, a helicogenic brush is less resistant to compression in the direction perpendicular to stretching due to easy alignment of helices and fewer unfavorable interactions between helical segments. At higher tethering density, the abovementioned stretch-induced decrease in helical content resists further compression. The proposed model is useful for understanding an emerging class of biomaterials that utilize helix-forming polymer brushes to induce shape changes or to stabilize biofunctional helical peptide sequences.     

Diblock polyampholytes grafted onto spherical particles: effect of stiffness, charge density, and grafting density

The structure of spherical brushes formed by symmetric diblock polyampholytes end-grafted onto small spherical particles in aqueous solution is examined within the framework of the so-called primitive model using Monte Carlo simulations. The properties of the two blocks are identical except for the sign of their charges. Three different chain flexibilities corresponding to flexible, semiflexible, and stiff blocks are considered at various polyampholyte linear charge densities and grafting densities. The link between the two blocks is flexible at all conditions, and the grafted segments are laterally mobile. Radial and lateral spatial distribution functions of different types and single-chain properties are analyzed. The brush structure strongly depends on the chain flexibility. With flexible chains, a disordered polyelectrolyte complex is formed at the surface of the particle, the complex becoming more compact at increasing linear charge density. With stiff blocks, the inner blocks are radially oriented. At low linear charged density, the outer blocks are orientationally disordered, whereas at increasing electrostatic interaction the two blocks of a polyampholyte are parallel and close to each other, leading to an ordered structure referred to as a polyampholyte star. As the grafting density is increased, the brush thickness responds differently for flexible and nonflexible chains, depending on a different balance between electrostatic interactions and excluded volume effects.     

Towards a mesoscopic model of water-like fluids with hydrodynamic interactions

We present a mesoscopic lattice model for non-ideal fluid flows with directional interactions, mimicking the effects of hydrogen bonds in water. The model supports a rich and complex structural dynamics of the orientational order parameter, and exhibits the formation of disordered domains whose size and shape depend on the relative strength of directional order and thermal diffusivity. By letting the directional forces carry an inverse density dependence, the model is able to display a correlation between ordered domains and low density regions, reflecting the idea of water as a denser liquid in the disordered state than in the ordered one.     

Effect of surface grafted polymers on the adsorption of different model proteins

Adsorption of a model protein to a surface with end-grafted polymers was studied by Monte Carlo simulations. In the model the effect on protein adsorption in the presence of end-grafted polymers was evaluated by calculating the change in free energy between an end-grafted surface and a surface without polymers. The change in free energy was calculated using statistical mechanical perturbation theory. Apart from ordinary athermal polymer-polymer and protein-polymer interactions we also study a broad selection of systems by varying the interaction between proteins and polymers and effective polymer-solvent interactions. The interactions between the molecules span an interval from -0.5 to +0.5 kT. Consequently, general features of protein adsorption to end-grafted surfaces is investigated by systematically changing properties like hydrophilicity/hydrophobicity of the polymer, protein and surface as well as grafting density, degree of polymerization and protein size. Increasing grafting density as well as degree of polymerization decreases the adsorption of protein except in systems with attractive polymer-protein interactions, where adsorption increases with increasing chain length and higher grafting density. At a critical polymer-protein interaction neither chain length nor grafting density affects the free energy of adsorption. Hydrophilic polymers were found to prevent adsorption better than hydrophobic polymers. Very small particles with radii comparable to the size of a polymer segment were, however, better excluded from the surface when using hydrophobic than hydrophilic polymers. For systems with attractive polymer-protein interaction not only the volume of the protein was shown to be of importance but also the size of the exposed surface.     

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.     

Effect of attractions on the structure of polymer solutions confined between surfaces: a density functional approach

A density functional theory is presented to study the effect of attractions on the structure of polymer solutions confined between surfaces. The polymer molecules have been modeled as a pearl necklace of freely jointed hard spheres and the solvent as hard spheres, both having Yukawa-type attractions and the mixture being confined between attractive Yukawa-type surfaces. The present theory treats the ideal gas free energy functional exactly and uses weighted density approximation for the hard chain and hard sphere contributions to the excess free energy functional. The attractive interactions are calculated using the direct correlation function obtained from the polymer reference interaction site model theory along with the mean spherical approximation closure. The theoretical predictions on the density profiles of the polymer and the solvent molecules are found to agree quite well with the Monte Carlo simulation results for varying densities, chain lengths, wall separations, and different sets of interaction potentials.     

Surface tension and scaling of critical nuclei in diatomic and triatomic fluids

Density functional theory has been used to investigate surface tension and scaling of critical clusters in fluids consisting of diatomic and rigid triatomic molecules. The atomic sites are hard spheres with attractive interactions obtained from the tail part of the Lennard-Jones potential. Asymmetry in attractive interactions between the atomic sites has been introduced to cause molecular orientation and oscillatory density profiles at liquid-vapor interfaces. The radial dependence of cluster surface tension in fluids showing modest orientation in unimolecular layer at the interface or no orientation at all resembles the surface tension behavior of clusters in simple monoatomic fluids, although the surface tension maximum becomes more pronounced with increasing chain length of the molecule. Surface tension of clusters having multiple oscillatory layers at the interface shows a prominent maximum at small cluster sizes; however, the surface tension of large clusters is lower than the planar value. The scaling relation for the number of molecules in the critical cluster and the nucleation barrier height developed by McGraw and Laaksonen [Phys. Rev. Lett. 76, 2754 (1996)] are well obeyed for fluids with little structure at liquid-vapor interface. However, fluids having enhanced interfacial structure show some deviation from the particle number scaling, and the barrier height scaling breaks up seriously.     

嵌段高分子尾形链构象性质的Monte Carlo研究

基于简立方格点模型对AB两嵌段高分子尾形链的构象性质及其链节的空间分布进行了MonteCarlo模拟.结果表明,链的尺寸、形状和链节的空间分布等统计性质和B链节与平面壁之间的相互吸引能有关.随着B链节与壁之间的吸引能的增加,链的尺寸和形状均呈现出先下降后升高的变化趋势,而且B链节的比例越大,这种变化越明显.     

Strength and Nature of Host-Guest Interactions in Metal-Organic Frameworks from a Quantum-Chemical Perspective

Metal-organic frameworks (MOFs) offer a convenient means for capturing, transporting, and releasing small molecules. Their rational design requires an in-depth understanding of the underlying non-covalent host-guest interactions, and the ability to easily and rapidly pre-screen candidate architectures in silico. In this work, we devised a recipe for computing the strength and analysing the nature of the host-guest interactions in MOFs. By assessing a range of density functional theory methods across periodic and finite supramolecular cluster scale we find that appropriately constructed clusters readily reproduce the key interactions occurring in periodic models at a fraction of the computational cost. Host-guest interaction energies can be reliably computed with dispersion-corrected density functional theory methods; however, decoding their precise nature demands insights from energy decomposition schemes and quantum-chemical tools for bonding analysis such as the quantum theory of atoms in molecules, the non-covalent interactions index or the density overlap regions indicator.     

On the inner structure and topology of clusters in two-component lipid bilayers. Comparison of monomer and dimer Ising models

It has been shown on model and biological systems that membrane clusters can affect in-plane membrane reactions and can control biochemical reaction cascades. Clusters of two-component phospholipid bilayers have been simulated by two Ising-type lattice models: the monomer and the dimer model. In each model the plane of one layer of the bilayer is represented by a triangular lattice, each site of which is occupied by an acyl chain of either a component 1 or a component 2 lipid molecule. The dimer model assumes that pairs of acyl chains (lipid molecules) are permanently connected, forming dimers on the lattice, while in the case of the monomer model this covalent connection between acyl chains is ignored. Phase diagrams of two-component phospholipid bilayers were successfully calculated by both models. In this work, we use Monte Carlo techniques to calculate thermodynamic averages of global and local characteristics of the largest component 2 cluster (such as outer/inner perimeter, percolation, minimal linear size, and local density) and compare the results obtained by the two models. A new method is developed to characterize the inner structure of the clusters. Each point of a cluster is classified based on its shortest distance (or depth) from the cluster's outer perimeter. Then local cluster properties, such as density, are calculated as a function of the depth. The depth analysis reveals that toward the cluster interior the average density usually decreases in midsize clusters and remains constant in very large clusters. On the basis of the simulations the following typical cluster topologies are identified at different cluster sizes and cooperativity parameter values: (i) branch-like, (ii) circular, (iii) band-like, and (iv) planar.We did not find qualitative differences between the cluster structures in the dimer and monomer model. However, at the same cluster size and cooperativity parameter value the cluster of the dimer model is more compact. The cluster properties of the dimer model are different from that of the monomer model because of the lower mixing entropy and higher formation energy of an elementary inner island.     

Structural evolution of subnano platinum clusters

We present a theoretical study of the structural evolution of small minimum energy platinum clusters, using density functional theory (DFT). Three growth pathways were identified. At the subnanoscale, clusters with triangular packing are energetically most favorable. At a cluster size of approximately n = 19, a structural transition from triangular clusters to icosahedral clusters occurs. A less energetically favorable transition from triangular clusters to fcc‐like clusters takes place at around n = 38. Ionization potentials, electron affinities, and magnetic moments of the triangular clusters were also calculated. Understanding the structures and properties will facilitate studies of the chemical reactivity of Pt nanoclusters toward small molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

On the equation of state for thermal polymer solutions and melts with attractive interaction

We perform Monte Carlo simulations of a lattice model for polymer melts, i. e., the bond fluctuation model in three dimensions. By using an energy parameter that prefers relatively long bonds, the model exhibits a glass transition at low temperatures, in close qualitative similarity to experiment. We modify this model by adding an attractive interaction of variable strength. We demonstrate that a small interaction strength has only a very small effect on the static properties of the melt. For a fixed strength of the potential, the chemical potential is measured by a modified particle-insertion method over a large range of temperatures and densities. The osmotic pressure is obtained by thermodynamic integration. In contrast to the original version our extended model exhibits a positive thermal expansion.     

Microphase separation in two-dimensional systems with competing interactions

The formation of clusters in condition of thermodynamic equilibrium can be easily observed both in two and three dimensions. In two dimensions relevant cases include pattern formation in Langmuir monolayers and ferrofluids, while in three dimensions cluster phases have been observed in colloids and in protein solutions. We have analyzed the problem within the scenario of competing interactions: typically, a short-range attractive interaction against a long-range repulsive one. This simplified approach is suggested by the fact that the forces, governing self-organization, act on a length scale which is larger than the molecular size; as a consequence many specific details of the molecules of interest are not necessary for studying the general features of microphases. We have tackled the microphase formation by simulations in bidimensional fluids, exploiting the parallel tempering scheme. In particular, we have analyzed the density range in which the particles arrange in circular domains (droplets), and the temperature range in which the system goes from microphases to the homogeneous fluid phase. As the density increases, the droplet size increases as well, but above a certain density the morphology changes and stripes are formed. Moreover at low density, we observe the formation of a liquidlike phase of disordered droplets; at higher densities, instead, the droplets tend to arrange onto a triangular superlattice. Such a change affects the features of the static structure factor, which gives well defined signatures of the microphase morphology. In each case, the specific heat exhibits a peak close to the transition from microphases to the homogeneous fluid phase, which is due to the breaking up of the clusters. The saturation of the height of the specific heat peak, with the increasing of the system size, suggests the possibility of a Kosterlitz-Thouless transition.     

Exploring the lower limit in hydrogen bonds: analysis of weak C-H...O and C-H...pi interactions in substituted coumarins from charge density analysis

Experimental electron densities in coumarin, 1-thiocoumarin, and 3-acetylcoumarin have been analyzed based on the X-ray diffraction data at 90 K. These compounds pack in the crystal lattice with weak C-H...O and C-H...pi interactions, and variations in charge density properties and derived local energy densities have been investigated in the regions of intermolecular interactions. Theoretical charge density calculations on crystals using the B3LYP/6-31G* method show remarkable agreement with the derived properties and energy densities from the experiment. The intermolecular interactions follow an exponential dependence of electron density and energy densities at the bond critical points. The Laplacian follows a "Morse-like" dependence on the length of the interaction line. Based on the set of criteria defined using the theory of "atoms in molecules", it has become possible to distinguish between a hydrogen bond (C-H...O) and a van der Waals interaction (C-H...pi). This has resulted in the identification of a "region of overlap" in terms of electron densities, energy densities, and mutual penetration of the hydrogen and acceptor atoms with respect to the interaction length. This approach suggests a possible tool to distinguish between the two types of interactions.     

Filled and empty states of carbon nanotubes in water: Dependence on nanotube diameter, wall thickness and dispersion interactions

We have carried out a series of molecular dynamics simulations of water containing a narrow carbon nanotube as a solute to investigate the filling and emptying of the nanotube and also the modifications of the density and hydrogen bond distributions of water inside and also in the vicinity of the outer surfaces of the nanotube. Our primary goal is to look at the effects of varying nanotube diameter, wall thickness and also solute-solvent interactions on the solvent structure in the confined region also near the outer surfaces of the solute. The thickness of the walls is varied by considering single and multi-walled nanotubes and the interaction potential is varied by tuning the attractive strength of the 12–6 pair interaction potential between a carbon atom of the nanotubes and a water molecule. The calculations are done for many different values of the tuning parameter ranging from fully Lennard-Jones to pure repulsive pair interactions. It is found that both the solvation characteristics and hydrogen bond distributions can depend rather strongly on the strength of the attractive part of the solute-water interaction potential. The thickness of the nanotube wall, however, is found to have only minor effects on the density profiles, hydrogen bond network and the wetting characteristics. This indicates that the long range electrostatic interactions between water molecules inside and on the outer side of the nanotube do not make any significant contribution to the overall solvation structure of these hydrophobic solutes. The solvation characteristics are primarily determined by the balance between the loss of energy due to hydrogen bond network disruption, cavity repulsion potential and offset of the same by attractive component of the solute-water interactions. Our studies with different system sizes show that the essential features of wetting and dewetting characteristics of narrow nanotubes for different diameter and interaction potentials are also present in relatively smaller systems consisting of about five hundred molecules. We dedicate this work to Professor Debashis Mukherjee on his 60th Birthday.     

Simulations of NaCl Aggregation from Solution: Solvent Determines Topography of Free Energy Landscape

The partition-enabled analysis of cluster histograms (PEACH) method is used to calculate the free energy surface of NaCl aggregation using cluster statistics from MD simulations of small systems (40–90 ions plus solvent) in four solvents. In all cases (pure methanol, pure water, and two methanol/water mixtures) NaCl clusters show a transition from amorphous to rocksalt structure with increasing cluster size. The crossover sizes, and the apparent kinetic barrier to ordering, increase with increasing water content. Implications for the proposed two-step mechanism of NaCl crystal nucleation (in which the ordered structure emerges from a large disordered cluster), and how this mechanism might depend on solvent and on degree of supersaturation, are discussed. In pure water, nonideal crowding effects that promote clustering are identified from systematic concentration-dependent deviations between simulation results and the PEACH model fit. In contrast, the ability of PEACH to fit aggregation statistics in mixed solvents is consistent with negligible interactions between ions in different clusters. © 2018 Wiley Periodicals, Inc.     

Hydrogen‐Bond Cooperative Effects in Small Cyclic Water Clusters as Revealed by the Interacting Quantum Atoms Approach

The cooperative effects of hydrogen bonding in small water clusters (H₂O)_n (n=3–6) have been studied by using the partition of the electronic energy in accordance with the interacting quantum atoms (IQA) approach. The IQA energy splitting is complemented by a topological analysis of the electron density (ρ( r )) compliant with the quantum theory of atoms‐in‐molecules (QTAIM) and the calculation of electrostatic interactions by using one‐ and two‐electron integrals, thereby avoiding convergence issues inherent to a multipolar expansion. The results show that the cooperative effects of hydrogen bonding in small water clusters arise from a compromise between: 1) the deformation energy (i.e., the energy necessary to modify the electron density and the configuration of the nuclei of the isolated water molecules to those within the water clusters), and 2) the interaction energy (E_int) of these contorted molecules in (H₂O)_n. Whereas the magnitude of both deformation and interaction energies is enhanced as water molecules are added to the system, the augmentation of the latter becomes dominant when the size of the cluster is increased. In addition, the electrostatic, classic, and exchange components of E_int for a pair of water molecules in the cluster (H₂O)_n?1 become more attractive when a new H₂O unit is incorporated to generate the system (H₂O)_n with the last‐mentioned contribution being consistently the most important part of E_int throughout the hydrogen bonds under consideration. This is opposed to the traditional view, which regards hydrogen bonding in water as an electrostatically driven interaction. Overall, the trends of the delocalization indices, δ(Ω,Ω′), the QTAIM atomic charges, the topology of ρ( r ), and the IQA results altogether show how polarization, charge transfer, electrostatics, and covalency contribute to the cooperative effects of hydrogen bonding in small water clusters. It is our hope that the analysis presented in this paper could offer insight into the different intra‐ and intermolecular interactions present in hydrogen‐bonded systems.     

Pdn(n=1-7)团簇及其与甲烷相互作用的密度泛函理论研究

用密度泛函理论(DFT)的B3LYP方法, 对Pdn(n=1-7)团簇的几何结构、振动频率及其与甲烷分子间的相互作用进行了理论研究. 结果表明, 随着Pd原子数增多, 团簇结构对团簇大小的依赖性减弱, 结构参数向金属晶体趋近. 在Pdn(n=1-7)团簇上, 甲烷的表面吸附作用较弱. Pd2CH4中, 甲烷受到两个Pd原子的活化作用, 活化程度增强, 吸附能增大. 在PdnCH4 (n=1, 3-7)体系中, 甲烷的吸附能随着团簇模型的增大而减小, 趋近于其在金属晶面上的吸附能.