Amino acid side chain interactions in the presence of salts

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0-2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf's) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf's are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed.     

Investigation of the local composition enhancement and related dynamics in supercritical CO2-cosolvent mixtures via computer simulation: the case of ethanol in CO2

The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local intermolecular structure of the fluid was studied in terms of the calculated appropriate pair radial distribution functions. The estimated average local coordination numbers and mole fractions around the species in the mixture reveal the existence of local composition enhancement of ethanol around the ethanol molecules. This finding indicates the nonideal mixing behavior of the mixture due to the existence of aggregation between the ethanol molecules. Furthermore, the local environment redistribution dynamics have been explored by analyzing the time correlation functions (TCFs) of the total local coordination number (solvent, cosolvent) around the cosolvent molecules in appropriate parts. The analysis of these total TCFs in the auto-(solvent-solvent, cosolvent-cosolvent) and cross-(solvent-cosolvent, cosolvent-solvent) TCFs has shown that the time dependent redistribution process of the first solvation shell of ethanol is mainly determined by the redistribution of the CO2 solvent molecules. These results might be explained on the basis of the CO2-CO2 and EtOH-CO2 intermolecular forces, which are sufficiently weaker in comparison to the EtOH-EtOH hydrogen bonding interactions, creating in this way a significantly faster redistribution of the CO2 molecules in comparison with EtOH. Finally, the self-diffusion coefficients and the single reorientational dynamics of both the cosolvent and solvent species in the mixture have been predicted and discussed in relationship with the local environment around the species, which in the case of the EtOH molecules seem to be strongly affected.     

Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics

The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer beads that is less than unity. In both solvent regimes the oligomer is found to extend in the direction of flow. Under the ideal solvent conditions, torsional twisting of the chain and aperiodic cyclical dynamics are observed for the end of the oligomer. Under poor solvent conditions, a metastable helix forms in the end of the chain despite the lack of any attractive potential between beads in the oligomeric chain. The formation of the helix is postulated to be the result of a solvent induced chain collapse that has been confined to a single dimension by a strong flow field.     

Friction and diffusion of a Brownian particle in a mesoscopic solvent

The friction and diffusion coefficients of a massive Brownian particle in a mesoscopic solvent are computed from the force and the velocity autocorrelation functions. The mesoscopic solvent is described in terms of free streaming of the solvent molecules, interrupted at discrete time intervals by multiparticle collisions that conserve mass, momentum, and energy. The Brownian particle interacts with the solvent molecules through repulsive Lennard-Jones forces. The decays of the force and velocity autocorrelation functions are analyzed in the microcanonical ensemble as a function of the number N of solvent molecules and Brownian particle mass and diameter. The simulations are carried out for large system sizes and long times to assess the N dependence of the friction coefficient. The decay rates of these correlations are confirmed to vary as N(-1) in accord with earlier predictions. Hydrodynamic effects on the velocity autocorrelation function and diffusion coefficient are studied as a function of Brownian particle mass and diameter.     

Coarse-grain model for lipid bilayer self-assembly and dynamics: Multiparticle collision description of the solvent

A mesoscopic coarse-grain model for computationally efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for the solvent. Self-assembly of a membrane from a uniform mixture of lipids is observed. Simulations at different temperatures demonstrate that it reproduces the gel and liquid phases of lipid bilayers. Investigations of lipid diffusion in different phases reveals a crossover from subdiffusion to normal diffusion at long times. Macroscopic membrane properties, such as stretching and bending elastic moduli, are determined directly from the mesoscopic simulations. Velocity correlation functions for membrane flows are determined and analyzed.     

Mesoscopic simulations on the aggregation behavior of pH-responsive polymeric micelles for drug delivery

Computer simulations, dissipative particle dynamics (DPD) and mesoscopic dynamics (MesoDyn), are performed to study the aggregation behavior of pH-sensitive micelles self-assembled from amphiphilic polymer poly(methyl methacrylate-co-methacrylic acid)-b-poly(poly-(ethylene glycol) methyl ether monomethacrylate), P(MMA-co-MAA)-b-PPEGMA. Ibuprofen (IBU) is selected as the model drug. It can be seen from DPD simulations that P(MMA-co-MAA)-b-PPEGMA and IBU form spherical core-shell micelles at certain compositions, and IBU molecules distribute inside the core formed by hydrophobic MMA. The polymer molecules aggregate first, and then IBU diffuses into the aggregate, forming drug-loaded nanoparticles. With different compositions of polymer and IBU, aggregate morphologies in water are observed as sphere, column and lamella. From MesoDyn results, with less hydrophobic MMA beads, the polymer chains are more difficult to form ordered aggregates, and the order parameters get equilibrated in a longer time. The pH value also affects the aggregate process. At pH<5, the polymer could form traditional core-shell micelles. But at pH>5, the morphology of micelles is found to be anomalous and loose for releasing drug. MAA aggregates on the surface, instead of the inside. The simulation results are qualitatively consistent with the experimental results.     

Single-chain and aggregation properties of semiconducting polymer solutions investigated by coarse-grained langevin dynamics simulation

A coarse-grained (CG) model and Langevin dynamics scheme are proposed to investigate the material properties in dilute solution of a model semiconducting conjugated polymer, poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV). While the intra- and intermolecular potentials for the CG particle (currently, a monomer unit) were determined from the molecular dynamics (MD) simulation of a united atomistic model, fluctuation-dissipation forces arising from the treatment of a solvent field were self-consistently constructed from the measured particle diffusivity in a given solvent (i.e., chloroform or toluene) through the atomistic MD simulation. It is shown that the resultant Langevin dynamics simulation, which is substantially more efficient than the counterpart MD simulation of the same CG model, is able to capture the dynamic (such as center-of-mass diffusivity) as well as the structural (such as radius of gyration) features of the investigated polymer solutions. Essential material properties that can now be directly studied include the following: Scaling exponents for estimating the exact solvent qualities were, for the first time, determined for the two solvent systems investigated; the persistence length obtained was also noted to be in excellent agreement with early experimental estimations. Preliminary observations on the supramolecular aggregation properties were in good agreement with the general observations from a wide range of recent experiments, and shed light on the essential impact of solvent quality on the supramolecular aggregation structures.     

Two-particle friction in a mesoscopic solvent

The effects of hydrodynamic interactions on the friction tensors for two particles in solution are studied. The particles have linear dimensions on nanometer scales and are either simple spherical particles interacting with the solvent through repulsive Lennard-Jones forces or are composite cluster particles whose atomic components interact with the solvent through repulsive Lennard-Jones forces. The solvent dynamics is modeled at a mesoscopic level through multiparticle collisions that conserve mass, momentum, and energy. The dependence of the two-particle relative friction tensors on the interparticle separation indicates the importance of hydrodynamic interactions for these nanoparticles.     

Design of chemically propelled nanodimer motors

The self-propelled motion of nanodimers fueled by a chemical reaction taking place under nonequilibrium steady state conditions is investigated. The nanodimer consists of a pair of catalytic and chemically inactive spheres, in general with different sizes, with a fixed internuclear separation. The solvent in which the dimer moves is treated at a particle-based mesoscopic level using multiparticle collision dynamics. The directed motion of the dimer can be controlled by adjusting the interaction potentials between the solvent molecules and the dimer spheres, the internuclear separation, and sphere sizes. Dimers can be designed so that the directed motion along the internuclear axis occurs in either direction and is much larger than the thermal velocity fluctuations, a condition needed for such nanodimers to perform tasks involving targeted dynamics.     

studies in the relationship between molecular structure and chromatographic behaviour-III Mechanism of the reversed-phase chromatography of some alkyl phenols

It can be shown that thin-layer chromatography by the reversed-phase technique gives results which are sufficiently reproducible for correlation of Chromatographie behaviour with chemical structure to be attempted. To a first approximation the Martin additivity principle is valid, but variations in the intermolecular forces between solute molecules and solvent molecules, caused by the easy transmission of electronic effects through an aromatic system, result in deviations from ideal conditions.     

NMR analysis of interaction between styrene-divinylbenzene gel beads and small molecules

The interaction of small molecules such as cyclohexane, tetrahydrofuran, and acetonitrile with styrene-divinylbenzene copolymer gel beads were investigated by ¹³C-NMR spectroscopy. When the gel content was 0.1–0.3 g/mL, the ¹³C-NMR spectrum of the solvent displayed two peaks. A sharp peak at lower magnetic field was assigned to the free solvent, and a broad one to the solvent affected by the gel. This signal splitting is attributed to the upfield shift caused by aromatic rings of styrene units in the polymer chain. The nitrile carbon of acetonitrile showed the largest upfield shift. The mobility of small molecules in gel beads was also investigated using the nuclear magnetic relaxation method. In the case of good solvents for gel beads, the mobility was affected by the cross-linking density, whereas poor solvents exhibited little dependence of the cross-linking density. © 1995 John Wiley & Sons, Inc.     

Complete mapping of the morphologies of some linear and graft fluorinated co-oligomers in an aprotic solvent by dissipative particle dynamics

The mesoscopic morphologies of linear and graft fluorinated block copolymers of ABCBA and C:BA types, respectively, have been investigated by using dissipative particle dynamics method. Self-assembly in a selective solvent has been examined by the introduction of dimethylformamide as the choice of solvent. By comparing the solubility parameters calculated using atomistic simulations, fluorine-containing segments are found to be immiscible both with other segments of the polymer and with the solvent. Morphologies of the pure linear and graft copolymers were lamellar and cylindrical, respectively. Interfacial tension versus concentration curves have been used to explain the self-assembly behavior of copolymers in solution, as well as to predict the kinetic mechanisms responsible for this behavior.     

Thermodynamic properties of some concentrated polymer solutions

Solubilities of several solvents were measured in four molten polymers by using an isobaric vapor-pressure apparatus. Solvent concentration ranged from 0.5 to 15 wt-%. The systems polyisoprene–benzene and polyisobutylene–benzene were studied at 80.0°C; polyisobutylene–cyclohexane was studied at 100.0°C; ethylene–vinyl acetate copolymer (EVA)–cyclohexane, EVA–isooctane, and poly(vinyl acetate)–isooctane were studied at 110.0°C. Of six polymer–solvent systems studied, all except poly(vinyl acetate)–isooctane appear to exhibit hysteresis in a single sorption–desorption cycle starting with dry polymer. The desorption curves of solvent activity plotted versus solvent weight fraction show an inflection point, suggesting localized adsorption of solvent molecules. Experimental data were analyzed with a theory which takes into account adsorption of solvent by polymer in addition to differences in free volumes and intermolecular forces. The theory gives a semiquantitative representation of the experimental data.     

Reconsideration on hydrogen bond strengthening or cleavage of photoexcited coumarin 102 in aqueous solvent: a DFT/TDDFT study

In this work, the excited-state hydrogen bonding dynamics of photoexcited coumarin 102 in aqueous solvent is reconsidered. The electronically excited states of the hydrogen bonded complexes formed by coumarin 102 (C102) chromophore and the hydrogen donating water solvent have been investigated using the time-dependent density functional theory method. Two intermolecular hydrogen bonds between C102 and water molecules are considered. The previous works (Wells et al., J Phys Chem A 2008, 112, 2511) have proposed that one intermolecular hydrogen bond would be strengthened and the other one would be cleaved upon photoexcitation to the electronically excited states. However, our theoretical calculations have demonstrated that both the two intermolecular hydrogen bonds between C102 solute and H(2)O solvent molecules are significantly strengthened in electronically excited states by comparison with those in ground state. Hence, we have confirmed again that intermolecular hydrogen bonds between C102 chromophore and aqueous solvents are strengthened not cleaved upon electronic excitation, which is in accordance with Zhao's works.     

An efficient ring polymer contraction scheme for imaginary time path integral simulations

A quantum simulation of an imaginary time path integral typically requires around n times more computational effort than the corresponding classical simulation, where n is the number of ring polymer beads (or imaginary time slices) used in the calculation. However, this estimate neglects the fact that the potential energies of many systems can be decomposed into a sum of rapidly varying short-range and slowly varying long-range contributions. For such systems, the computational effort of the path integral simulation can be reduced considerably by evaluating the long-range forces on a contracted ring polymer with fewer beads than are needed to evaluate the short-range forces. This idea is developed and then illustrated with an application to a flexible model of liquid water in which the intramolecular forces are evaluated with 32 beads, the oxygen-oxygen Lennard-Jones forces with seven, and the intermolecular electrostatic forces with just five. The resulting static and dynamic properties are within a few percent of those of a full 32-bead calculation, and yet they are obtained with a computational effort less than six times (rather than 32 times) that of a classical simulation. We hope that this development will encourage future studies of quantum mechanical fluctuations in liquid water and aqueous solutions and in many other systems with similar interaction potentials.     

Universal consequences of the presence of excluded volume interactions in dilute polymer solutions undergoing shear flow

The role of solvent quality in determining the universal material properties of dilute polymer solutions undergoing steady simple shear flow is examined. A bead-spring chain representation of the polymer molecule is used, and the influence of solvent molecules on polymer conformations is modelled by a narrow Gaussian excluded volume potential that acts pairwise between the beads of the chain. Brownian dynamics simulations data, acquired for chains of finite length, and extrapolated to the limit of infinite chain length, are shown to be model independent. This feature of the narrow Gaussian potential, which leads to results identical to a delta-function repulsive potential, enables the prediction of both universal crossover scaling functions and asymptotic behavior in the excluded volume limit. Universal viscometric functions, obtained by this procedure, are found to exhibit increased shear thinning with increasing solvent quality. In the excluded volume limit, they are found to obey power law scaling with the characteristic shear rate beta, in close agreement with previously obtained renormalization group results. The presence of excluded volume interactions is also shown to lead to a weakening of the alignment of the polymer chain with the flow direction.     

Microphase separation in two-dimensional athermal polymer solutions on a triangular lattice

The results of Monte Carlo simulations of 2D polymer solutions are presented. The simulations were performed under athermal conditions for long chains (up to 1024 beads) over a full range of polymer concentration phi, explicitly taking into account the solvent molecules. The results obtained for short chains (N < or = 256) are in good agreement with previous simulations whereas for long chains microphase separation is observed below phi = 0.6. This phenomenon is attributed to strong excluded volume interactions in 2D systems. A sort of interpenetration of the coils is also observed.     

Self‐Alignment of Beads and Cell Trapping in Precipitate Tubes

Propagating reaction fronts allow the formation of materials in self‐sustained, steep concentration gradients, which would otherwise rapidly decay. These conditions can result in macroscopic, noncrystallographic structures, such as tubes with large aspect ratios. For hollow silica/Zn(OH)₂ tubes, we report the inclusion of diverse mesoscopic building blocks ranging from polymer beads to biological cells. For agarose beads, we observe spontaneous alignment along vertical tracks; the nearly periodic spacing of the beads along these tracks follows a log‐normal distribution. We interpret this patterning in terms of hydrodynamic recruitment and discuss similarities to the adhesion dynamics of leukocytes in blood vessels. For diatoms and other cells, we observe novel surface textures, and yeast tagged with a green fluorescent protein shows strong fluorescence activity after trapping. The inclusion of these guest units should improve the possibilities for the application of these tubes in microfluidics and biotechnology.     

Conformation and diffusion behavior of ring polymers in solution: a comparison between molecular dynamics, multiparticle collision dynamics, and lattice Boltzmann simulations

We have studied the effect of chain topology on the structural properties and diffusion of polymers in a dilute solution in a good solvent. Specifically, we have used three different simulation techniques to compare the chain size and diffusion coefficient of linear and ring polymers in solution. The polymer chain is modeled using a bead-spring representation. The solvent is modeled using three different techniques: molecular dynamics (MD) simulations with a particulate solvent in which hydrodynamic interactions are accounted through the intermolecular interactions, multiparticle collision dynamics (MPCD) with a point particle solvent which has stochastic interactions with the polymer, and the lattice Boltzmann method in which the polymer chains are coupled to the lattice fluid through friction. Our results show that the three methods give quantitatively similar results for the effect of chain topology on the conformation and diffusion behavior of the polymer chain in a good solvent. The ratio of diffusivities of ring and linear polymers is observed to be close to that predicted by perturbation calculations based on the Kirkwood hydrodynamic theory.