Density functional theory for the recognition of polymer at nanopatterned surface

The recognition of homopolymer at nanopatterned surface has been investigated by density functional theory (DFT). Chain conformation and pattern transfer parameter predicted from the DFT are in good agreement with Monte Carlo simulation results. The theory describes satisfactorily the transition from depletion at low packing fractions to adsorption and double-layer adsorption at high packing fractions and also accounts for the crucial effect of the segment-wall interaction. It is found that homopolymer is better recognized at a low bulk density and a stronger interaction with the surface. The polymer can not only recognize the surface but also invert the surface at high bulk densities. The chain in the solution-wall interface exhibits a typical "brush" conformation with a length approximated by half the length of polymer chain.     

Rapid calculation of partition functions and free energies of fluids

The partition function (Q) is a central quantity in statistical mechanics. All the thermodynamic properties can be derived from it. Here we show how the partition function of fluids can be calculated directly from simulations; this allows us to obtain the Helmholtz free energy (F) via F = -k(B)T ln Q. In our approach, we divide the density of states, assigning half of the configurations found in a simulation to a high-energy partition and half to a low-energy partition. By recursively dividing the low-energy partition into halves, we map out the complete density of states for a continuous system. The result allows free energy to be calculated directly as a function of temperature. We illustrate our method in the context of the free energy of water.     

Density functional theory of homopolymer mixtures confined in a slit

A density functional theory (DFT) is developed for polymer mixtures with shorted-ranged attractive interparticle interactions confined in a slit. Different weighting functions are used separately for the repulsive part and the attractive part of the excess free energy functional by applying the weighted density approximation. The predicted results by DFT are in good agreement with the corresponding simulation data indicating the reliability of the theory. Furthermore, the center-of-mass profiles and the end-to-end distance distributions are obtained by the single chain simulation; the predictions also agree well with simulation data. The results reveal that both the attraction of the slit wall and the temperature has stronger effect on longer chains than on shorter ones because the intrasegment correlation of chains increases with increasing chain length.     

Adsorption of copolymers in a selective nanoslit: a hybrid density functional theory

A hybrid density functional theory (DFT) is developed for adsorption of copolymers in a selective nanoslit. The DFT incorporates a single-chain simulation for the ideal-gas free energy functional with two weighted density approximations for the residual free energy functional. The theory is found to be insensitive to the width parameter used in the weighted density. Theoretical predictions are in excellent agreement with simulation results in the segment density profiles and the adsorption configurations including tail, loop, and train for copolymers with various sequences over a wide range of surface affinity. The bridge conformation is also observed in multiblock copolymers. Ordered assembly is facilitated in copolymers with longer chain/block and at stronger attraction between segment B and the slit wall. While diblock copolymer shows the longest tail, alternating copolymer has the shortest. As the attraction between segment B and the slit wall increases, the average size and fraction decrease for tail, but increase for loop and train.     

Potentiometric selectivity coefficients of liquid ion-exchange membranes for univalent and divalent ions

Digital simulation has been used to calculate potential—activity responses and concentration-dependent selectivity coefficients for membranes bathed in mixtures of univalent and divalent ions. For an ideal, dissociated, univalent-site liquid ion-exchange membrane, more accurate computations, based on Nernst—Planck equations, were possible than have been reported previously. Simulation results were used with four suggested equations for the membrane potential (including the IUPAC recommendation) to determine which equation gives best fit and most nearly constant selectivity coefficients. When concentration profiles found by digital simulation are employed, improved response equations are given which closely describe the dependence of surface concentrations on the mobility ratio for the bi-ionic case. From these equations a closed form solution to the diffusion equation yields an explicit expression relating the bi-ionic selectivity coefficient to membrane loading, single ion partition coefficients, and ion mobilities.     

Density functional theory for copolymers confined in a nanoslit

A density functional theory is developed for copolymers confined in a nanoslit on the basis of our previous work for homopolymers. The theory accurately captures the structural characteristics for diblock and alternating copolymers composed of hard-sphere or square-well segments. Satisfactory agreement is obtained between the theoretical predictions and simulation results in segment density profiles, segment fractions, and partition coefficients. Structures under confinement strongly depend on the substituent segment sizes for the hard-sphere copolymers and also on the segment-wall attractions for the square-well copolymers. Alternating copolymers are found to behave as homopolymers with effective segment size, and effective segment-segment and segment-wall interactions.     

Polymer density functional theory approach based on scaling second-order direct correlation function

A second-order direct correlation function (DCF) from solving the polymer-RISM integral equation is scaled up or down by an equation of state for bulk polymer, the resultant scaling second-order DCF is in better agreement with corresponding simulation results than the un-scaling second-order DCF. When the scaling second-order DCF is imported into a recently proposed LTDFA-based polymer DFT approach, an originally associated adjustable but mathematically meaningless parameter now becomes mathematically meaningful, i.e., the numerical value lies now between 0 and 1. When the adjustable parameter-free version of the LTDFA is used instead of the LTDFA, i.e., the adjustable parameter is fixed at 0.5, the resultant parameter-free version of the scaling LTDFA-based polymer DFT is also in good agreement with the corresponding simulation data for density profiles. The parameter-free version of the scaling LTDFA-based polymer DFT is employed to investigate the density profiles of a freely jointed tangent hard sphere chain near a variable sized central hard sphere, again the predictions reproduce accurately the simulational results. Importance of the present adjustable parameter-free version lies in its combination with a recently proposed universal theoretical way, in the resultant formalism, the contact theorem is still met by the adjustable parameter associated with the theoretical way.     

Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study

Grand canonical ensemble Monte Carlo simulation (GCMC) combined with the histogram reweighting technique was used to study the thermodynamic equilibrium of a homopolymer solution between a bulk and a slit pore. GCMC gives the partition coefficients that agree with those from canonical ensemble Monte Carlo simulations in a twin box, and it also gives results that are not accessible through the regular canonical ensemble simulation such as the osmotic pressure of the solution. In a bulk polymer solution, the calculated osmotic pressure agrees very well with the scaling theory predictions both for the athermal polymer solution and the theta solution. However, one cannot obtain the osmotic pressure of the confined solution in the same way since the osmotic pressure of the confined solution is anisotropic. The chemical potentials in GCMC simulations were found to differ by a translational term from the chemical potentials obtained from canonical ensemble Monte Carlo simulations with the chain insertion method. This confirms the equilibrium condition of a polymer solution partition between the bulk and a slit pore: the chemical potentials of the polymer chain including the translational term are equal at equilibrium. The histogram reweighting method enables us to obtain the partition coefficients in the whole range of concentrations based on a limited set of simulations. Those predicted bulk-pore partition coefficient data enable us to perform further theoretical analysis. Scaling predictions of the partition coefficient at different regimes were given and were confirmed by the simulation data.     

Structure of Lennard-Jones fluids confined in square nanoscale channels from density functional theory

The density distribution of Lennard-Jones fluids confined in square nanoscale channels with Lennard-Jones walls has been studied using the nonlocal density functional theory (DFT) based on the Tarazona model. The effect of channel lengths on the density profiles with various chemical potentials was discussed. It was found that there is an apparent layering phenomenon for the confined fluids due to the combining influences of the enhancing solid-fluid interaction and the excluded volume effect. The pronounced density peaks were observed at the corners of square channels due to the strong fluid-solid interactions. The grand canonical ensemble Monte Carlo simulation (GCEMC) was applied to test the nonlocal DFT results. The DFT calculations are in relatively good agreement with the GCEMC simulations. The adsorption isotherms in a series of square channels were evaluated based on the obtained density distributions. The adsorption mechanism within the square pores was investigated. A comparison between the adsorptions of the square pores with those of the corresponding slit-size pores has been given.     

Comparison of two simulation methods to compute solvation free energies and partition coefficients

The thermodynamic integration (TI) and expanded ensemble (EE) methods are used here to calculate the hydration free energy in water, the solvation free energy in 1‐octanol, and the octanol‐water partition coefficient for a six compounds of varying functionality using the optimized potentials for liquid simulations (OPLS) all‐atom (AA) force field parameters and atomic charges. Both methods use the molecular dynamics algorithm as a primary component of the simulation protocol, and both have found wide applications in fields such as the calculation of activity coefficients, phase behavior, and partition coefficients. Both methods result in solvation free energies and 1‐octanol/water partition coefficients with average absolute deviations (AAD) from experimental data to within 4 kJ/mol and 0.5 log units, respectively. Here, we find that in simulations the OPLS‐AA force field parameters (with fixed charges) can reproduce solvation free energies of solutes in 1‐octanol with AAD of about half that for the solute hydration free energies using a extended simple point charge (SPC/E) model of water. The computational efficiency of the two simulation methods are compared based on the time (in nanoseconds) required to obtain similar standard deviations in the solvation free energies and 1‐octanol/water partition coefficients. By this analysis, the EE method is found to be a factor of nine more efficient than the TI algorithm. For both methods, solvation free energy calculations in 1‐octanol consume roughly an order of magnitude more CPU hours than the hydration free energy calculations. © 2012 Wiley Periodicals, Inc.     

Preferential interaction between DNA and small ions in mixed-size counterion systems: Monte Carlo simulation and density functional study

Competitive binding between counterions around DNA molecule is characterized using the preferential interaction coefficient of individual ion in single and mixed electrolyte solutions. The canonical Monte Carlo (MC) simulation, nonlinear Poisson-Boltzmann (PB) equation, and density functional theory (DFT) proposed in our previous work [Wang, Yu, Gao, and Luo, J. Chem. Phys. 123, 234904 (2005)] are utilized to calculate the preferential interaction coefficients. The MC simulations and theoretical results show that for single electrolyte around DNA, the preferential interaction coefficient of electrolyte decreases as the cation size is increased, indicating that the larger cation has less accumulation ability in the vicinity of DNA. For the mixed electrolyte solution, it is found that cation diameter has a significant effect on the competitive ability while anion diameter has a negligible effect. It proves that the preferential interaction coefficients of all ions decrease as the total ionic concentration is increased. The DFT generally has better performance than the PB equation does when compared to the MC simulation data. The DFT behaves quite well for the real ionic solutions such as the KCl-NaCl-H2O, NaCl-CaCl2-H2O, and CaCl2-MgCl2-H2O systems.     

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.     

Further test of third order + second-order perturbation DFT approach: hard core repulsive Yukawa fluid subjected to diverse external fields

Grand canonical Monte Carlo simulation is used to investigate density profiles of hard-core repulsive Yukawa (HCRY) model fluid under the influence of various external fields and radial distribution function (RDF) of the bulk HCRY system. The aim of these extensive simulations is to provide exact data for purely repulsive interaction potential against which the validity of a third order + second-order perturbation DFT approach can be tested. It is found that a semiempirical parametrized bridge function due to Malijevsky and Labik performs very well for the RDF of the bulk HCRY fluid. Incorporation of a bulk second-order direct correlation function (DCF) of the HCRY fluid based on the Malijevsky-Labik bridge function into the third order + second-order perturbation DFT approach yields the resulting theoretical predictions for the density profiles of inhomogeneous HCRY fluid that are in a very good agreement with the simulation data, an exception being somewhat larger deviations appearing for the structure of the fluid around the center of a hard spherical cavity. Both theory and simulation predict layering transition and gas-liquid coexistence phenomena occurring with the HCRY model fluid under confined conditions. For the case of an inverse sixth-power repulsive potential under the influence of a flat stationary wall defined by an inverse twelfth-power repulsive potential, the present third order + second-order perturbation DFT approach is found to be superior to several existing weighted density approximations (WDA) and partitioned WDA.     

Density profiles and solvation forces for a Yukawa fluid in a slit pore

The effect of varying wall-particle and particle-particle interactions on the density profiles near a single wall and the solvation forces between two walls immersed in a fluid of particles is investigated by grand canonical Monte Carlo simulations. Attractive and repulsive particle-particle and particle-wall interactions are modeled by a versatile hard-core Yukawa form. These simulation results are compared to theoretical calculations using the hypernetted chain integral equation technique, as well as with fundamental measure density functional theory (DFT), where particle-particle interactions are either treated as a first order perturbation using the radial distribution function or else with a DFT based on the direct-correlation function. All three theoretical approaches reproduce the main trends fairly well, but exhibit inconsistent accuracy, particularly for attractive particle-particle interactions. We show that the wall-particle and particle-particle attractions can couple together to induce a nonlinear enhancement of the adsorption and a related "repulsion through attraction" effect for the effective wall-wall forces. We also investigate the phenomenon of bridging, where an attractive wall-particle interaction induces strongly attractive solvation forces.     

Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model

A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic functional Taylor expansion around a uniform fluid. The electroneutrality in the cell leads to a variational equation with a constraint. Since the reference fluid is selected to be a bulk phase, the Lagrange multiplier proves to be the potential drop across the cell boundary (Donnan potential). The ion profiles and electrostatic potential profiles in the cell are calculated from the present DFT-cell model. Our DFT-cell model gives better prediction of ion profiles than the Poisson-Boltzmann (PB)- or modified PB-cell models when compared to the molecular simulation data. The effects of polyelectrolyte concentration, ion size, and added-salt concentration on the electrostatic potential difference between the DNA surface and the cell boundary are investigated. The expression of osmotic coefficient is derived from the general formula of grand potential. The osmotic coefficients predicted by the DFT are lower than the PB results and are closer to the simulation results and experimental data.     

Structure and adsorption of a hard-core multi-Yukawa fluid confined in a slitlike pore: grand canonical Monte Carlo simulation and density functional study

Because of the increasing interest in studying the phenomenon exhibited by charge-stabilized colloidal suspensions in confining geometry, we present a density functional theory (DFT) for a hard-core multi-Yukawa fluid. The excess Helmholtz free-energy functional is constructed by using the modified fundamental measure theory and Rosenfeld's perturbative method, in which the bulk direct correlation function is obtained from the first-order mean spherical approximation. To validate the established theory, grand canonical ensemble Monte Carlo (GCMC) simulations are carried out to determine the density profiles and surface excesses of multi-Yukawa fluid in a slitlike pore. Comparisons of the theoretical results with the GCMC data suggest that the present DFT gives very accurate density profiles and surface excesses of multi-Yukawa fluid in the slitlike pore as well as the radial distribution functions of the bulk fluid. Both the DFT and the GCMC simulations predict the depletion of the multi-Yukawa fluid near a nonattractive wall, while the mean-field theory fails to describe this depletion in some cases. Because the simple form of the direct correlation function is used, the present DFT is computationally as efficient as the mean-field theory, but reproduces the simulation data much better than the mean-field theory.     

Quantum versus classical electron transfer energy as reaction coordinate for the aqueous Ru2+/Ru3+ redox reaction

Applying density functional theory (DFT)-based molecular dynamics simulation methods we investigate the effect of explicit treatment of electronic structure on the solvation free energy of aqueous Ru²⁺ and Ru³⁺.Our approach is based on the Marcus theory of redox half reactions, focussing on the vertical energy gap for reduction or oxidation of a single aqua ion. We compare the fluctuations of the quantum and classical energy gap along the same equilibrium ab initio molecular dynamics trajectory for each oxidation state. The classical gap is evaluated using a standard point charge model for the charge distribution of the solvent molecules (water). The quantum gap is computed from the full DFT electronic ground state energies of reduced and oxidized species, thereby accounting for the delocalization of the electron in the donor orbital and reorganization of the electron cloud after electron transfer (ET). The fluctuations of the quantum ET energy are well approximated by gaussian statistics giving rise to parabolic free energy profiles. The curvature is found to be independent of the oxidation state in agreement with the linear response assumption underlying Marcus theory. By contrast, the diabatic free energy curves evaluated using the classical gap as order parameter, while also quadratic, are asymmetric reflecting the difference in oxidation state. The response of these two order parameters is further analysed by a comparison of the spectral density of the fluctuations and the corresponding reorganization free energies.     

Partition coefficients of organic molecules in squalane and water/ethanol mixtures by molecular dynamics simulations

Accurate partition coefficient data of migrants between a polymer and a solvent are of paramount importance for estimating the migration of the migrant over time, including the concentration of the migrant at infinite time in the two solvents. In this article it is shown how this partition coefficient can be estimated for both a small hydrophilic and a hydrophobic organic molecules between squalane (used here to mimic low density poly ethylene) and water/ethanol solutes using thermodynamic integration to calculate the free energy of solvation. Molecular dynamics simulations are performed, using the GROMACS software, by slowly decoupling of firstly the electrostatic and then the Lennard-Jones interactions between molecules in the simulation box. These calculations depend very much on the choice of force field. Two force fields have been tested in this work, the TraPPE-UA (united-atom) and the OPLS-AA (all-atom). The computational cheaper TraPPE-UA force field showed to be more accurate over the whole range of systems compared to the OPLS-AA force field. Moreover, some of the calculations were done with five different water models to investigate the influence of the specific water model on the calculations. It was found that the combination of the TraPPE-UA force field and the TIP4p water model gave the best results. Based on the methodology proposed in this article, it is possible to obtain good partition coefficients only knowing the chemical structure of the molecules in the system.