Hydrodynamic screening near planar boundaries: effects on semiflexible polymer dynamics

The influence of hydrodynamic screening near a surface on the dynamics of a single semiflexible polymer is studied by means of Brownian dynamics simulations and hydrodynamic mean field theory. The polymer motion is characterized in terms of the mean squared displacements of the end-monomers, the end-to-end vector, and the scalar end-to-end distance. In order to control hydrodynamic screening effects, the polymer is confined to a plane at a fixed separation from the wall. When gradually decreasing this separation, a crossover from Zimm-type towards Rouse (free-draining) polymer dynamics is induced. However, this crossover is rather slow and the free-draining limit is not completely reached--substantial deviations from Rouse-like dynamics are registered in both simulations and theory--even at distances of the polymer from the wall on the order of the monomer size. Remarkably, the effect of surface-induced screening of hydrodynamic interactions sensitively depends on the type of dynamic observable considered. For vectorial quantities such as the end-to-end vector, hydrodynamic interactions are important and therefore surface screening effects are sizeable. For a scalar quantity such as the end-to-end distance, on the other hand, hydrodynamic interactions are less important, but a pronounced dependence of dynamic scaling exponents on the persistence length to contour length ratio becomes noticeable. Our findings are discussed against the background of single-molecule experiments on f-actin [L. Le Goff et al., Phys. Rev. Lett. 89, 258101 (2002)].     

Resummed thermodynamic perturbation theory for central force associating potential. Multi-patch models

A resummed thermodynamic perturbation theory for associating fluids with multiply bondable central force associating potential is extended for the fluid with multiple number of multiply bondable associating sites. We consider a multi-patch hard-sphere model for associating fluids. The model is represented by the hard-sphere fluid system with several spherical attractive patches on the surface of each hard sphere. Resummation is carried out to account for blocking effects, i.e., when the bonding of a particle restricts (blocks) its ability to bond with other particles. Closed form analytical expressions for thermodynamical properties (Helmholtz free energy, pressure, internal energy, and chemical potential) of the models with arbitrary number of doubly bondable patches at all degrees of the blockage are presented. In the limiting case of total blockage, when the patches become only singly bondable, our theory reduces to Wertheim's thermodynamic perturbation theory (TPT) for polymerizing fluids. To validate the accuracy of the theory we compare to exact values, for the thermodynamical properties of the system, as determined by Monte Carlo computer simulations. In addition we compare the fraction of multiply bonded particles at different values of the density and temperature. In general, predictions of the present theory are in good agreement with values for the model calculated using Monte Carlo simulations, i.e., the accuracy of our theory in the case of the models with multiply bondable sites is similar to that of Wertheim's TPT in the case of the models with singly bondable sites.     

Solvent effects and dynamic averaging of 195Pt NMR shielding in cisplatin derivatives

The influences of solvent effects and dynamic averaging on the (195)Pt NMR shielding and chemical shifts of cisplatin and three cisplatin derivatives in aqueous solution were computed using explicit and implicit solvation models. Within the density functional theory framework, these simulations were carried out by combining ab initio molecular dynamics (aiMD) simulations for the phase space sampling with all-electron relativistic NMR shielding tensor calculations using the zeroth-order regular approximation. Structural analyses support the presence of a solvent-assisted "inverse" or "anionic" hydration previously observed in similar square-planar transition-metal complexes. Comparisons with computationally less demanding implicit solvent models show that error cancellation is ubiquitous when dealing with liquid-state NMR simulations. After aiMD averaging, the calculated chemical shifts for the four complexes are in good agreement with experiment, with relative deviations between theory and experiment of about 5% on average (1% of the Pt(II) chemical shift range).     

Equation of state for Lennard–Jones flexible ring fluids

We present a new equation of state for Lennard–Jones (LJ) flexible ring fluids. We perform Monte-Carlo simulations for freely-jointed Lennard–Jones chain fluids (3-, 6- and 8-mer) in the canonical ensemble and obtain the intramolecular end-to-end pair correlation function data under extensive density and temperature conditions. We correlate these as a function of the density, the temperature and the number of segments in a chain. We apply this function to thermodynamic perturbation theory (TPT) and obtain a new equation of state for Lennard–Jones flexible ring fluids. We also compare existing simulation data [J. Chem. Phys. 104 (1996) 1729] with the results obtained using the newly derived equation of state.     

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.     

Performance evaluation of third-order thermodynamic perturbation theory and comparison with existing liquid state theories

To evaluate the performance of a recently proposed third-order thermodynamic perturbation theory (TPT), we employ the third TPT for calculation of thermodynamic properties such as compressibility factor, internal energy, excess chemical potential, gas-liquid coexistence curve, and critical properties of several fluids. By comparing the third-order TPT results with corresponding simulation data available in literature and supplied in the present report and theoretical results from several other theoretical approaches, one concludes that the third-order TPT is, in general, more accurate than other approaches such as Barker-Henderson second-order TPT using a macroscopic compressibility approximation (MCA-TPT), self-consistent Ornstein-Zernike approach, Monte Carlo perturbation theory, and a specially devised equation of state. Specifically, the third-order TPT can predict quantitatively a double critical phenomena of gas-liquid transition and a low-density liquid (LDL)-high-density liquid (HDL) transition associated with a soft core (SC) potential fluid very satisfactorily, but the predictions for the LDL-HDL transition based on the second-order MCA-TPT are quantitatively very bad or qualitatively incorrect. The failure of the second-order MCA-TPT for the SC fluid can be ascribed to the facts that for the SC potential the second-order and third-order terms of the perturbation expansion are not small quantities and that the second-order term is underestimated by the MCA. It is concluded that the present third-order version of the TPT is reliable for varying model fluids.     

Comparison of implicit solvent models for the simulation of protein-surface interactions

Empirical force field-based molecular simulations can provide valuable atomistic-level insights into protein-surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface-separation distance for peptide-surface interactions using different empirical force field-based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self-consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement.     

On the dynamics of electrochemical ion-transfer reactions

A model electrochemical ion-transfer reaction is investigated by molecular dynamics simulations. Non-equilibrium solvation effects can lead to barrier recrossings when the ion passes the transition state. The resulting transmission coefficient, which measures the deviation of the rate from the predictions of the transition state theory, is in good agreement with the Grote–Hynes theory. By contrast, Kramers theory predicts a much lower rate constant. The reaction occurs in the polarization caging regime of Grote–Hynes theory, in which the solvent motion controls the advance of the reaction. Furthermore, the molecular friction depends strongly on the distance from the electrode.     

Solvation force, structure and thermodynamics of fluids confined in geometrically rough pores

The effect of periodic surface roughness on the behavior of confined soft sphere fluids is investigated using grand canonical Monte Carlo simulations. Rough pores are constructed by taking the prototypical slit-shaped pore and introducing unidirectional sinusoidal undulations on one wall. For the above geometry our study reveals that the solvation force response can be phase shifted in a controlled manner by varying the amplitude of roughness. At a fixed amplitude of roughness, a, the solvation force for pores with structured walls was relatively insensitive to the wavelength of the undulation, lambda for 2.3/=0.5. The predictions of the superposition approximation, where the solvation force response for the rough pores is deduced from the solvation force response of the slit-shaped pores, was in excellent agreement with simulation results for the structured pores and for lambda/sigma(ff)>/=7 in the case of smooth walled pores. Grand potential computations illustrate that interactions between the walls of the pore can alter the pore width corresponding to the thermodynamically stable state, with wall-wall interactions playing an important role at smaller pore widths and higher amplitudes of roughness.     

Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation

We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.     

Theory of repulsive charged colloids in slit-pores

Using classical density functional theory (DFT) we analyze the structure of the density profiles and solvation pressures of negatively charged colloids confined in slit pores. The considered model, which was already successfully employed to study a real colloidal (silica) suspension [S. H. L. Klapp et al., Phys. Rev. Lett. 100, 118303 (2008)], involves only the macroions which interact via the effective Derjaguin-Landau-Verwey-Overbeek (DLVO) potential supplemented by a hard core interaction. The solvent enters implicitly via the screening length of the DLVO interaction. The free energy functional describing the colloidal suspension consists of a hard sphere contribution obtained from fundamental measure theory and a long range contribution which is treated using two types of approximations. One of them is the mean field approximation (MFA) and the remaining is based on Rosenfeld's perturbative method for constructing the Helmholtz energy functional. These theoretical calculations are carried out at different bulk densities and wall separations to compare finally to grand canonical Monte Carlo simulations. We also consider the impact of charged walls. Our results show that the perturbative DFT method yields generally qualitatively consistent and, for some systems, also quantitatively reliable results. In MFA, on the other hand, the neglect of charge-induced correlations leads to a breakdown of this approach in a broad range of densities.     

Density functional theory of solvation and its relation to implicit solvent models

We describe a density functional theory approach to solvation in molecular solvents. The solvation free energy of a complex solute can be obtained by direct minimization of a density functional, instead of the thermodynamic integration scheme necessary when using atomistic simulations. In the homogeneous reference fluid approximation, the expression of the free-energy functional relies on the knowledge of the direct correlation function of the pure solvent. After discussing general molecular solvents, we present a generic density functional describing a dipolar solvent and we show how it can be reduced to the conventional implicit solvent models when the solvent microscopic structure is neglected. With respect to those models, the functional includes additional effects such as the microscopic structure of the solvent, the dipolar saturation effect, and the nonlocal character of the dielectric constant. We also show how this functional can be minimized numerically on a three-dimensional grid around a solute of complex shape to provide, in a single shot, both the average solvent structure and the absolute solvation free energy.     

Simulation and model development for the equation of state of heteronuclear non‐additive copolymer chains

Molecular dynamics simulations of hard alternating copolymer chains composed of size asymmetric nonadditive segments were performed. Different degrees of polymerization, densities, size ratios and nonadditivities were used. The equation of state for these copolymers was investigated and models based on the first order thermodynamic perturbation theory (TPT1) and the polymeric analog of the Percus‐Yevick approximation (PPY) were developed to predict the compressibility factor of the copolymers. The models predicted the compressibilities of the mixtures accurately at small size ratios, low degrees of polymerization and higher densities. The TPT1 model was generally more accurate in predicting the compressibility factor than the PPY model.     

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory provides a good approximation to Poisson electrostatic solvation energy calculations if one uses the same definitions of molecular volume for each. In this work, we present a new and improved analytic method for reproducing the Lee-Richards molecular volume, which is the most common volume definition for Poisson calculations. Overall, 1% errors are achieved for absolute solvation energies of a large set of proteins and relative solvation energies of protein conformations. We also introduce an accurate SASA approximation that uses the same machinery employed by our GB method and requires a small addition of computational cost. The combined methodology is shown to yield an efficient and accurate implicit solvent representation for simulations of biopolymers.     

Single wall carbon nanotubes density of states: comparison of experiment and theory

We study the electronic structure of a variety of single wall carbon nanotubes and report density of states obtained with the Perdew–Burke–Ernzerhof (PBE) generalized gradient approximation and hybrid PBE0 approximation of density functional theory using Gaussian orbitals and periodic boundary conditions. PBE gives very good results for metallic tubes but the addition of a portion of exact exchange in the hybrid PBE0 functional worsens the agreement between experiment and theory. On the other hand, the PBE0 hybrid significantly improves the theoretical predictions (compared to PBE) for semiconducting tubes.     

Universal properties of a single polymer chain in slit: Scaling versus molecular dynamics simulations

We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyze their range of validity by means of comprehensive molecular dynamics simulations using a coarse-grained bead-spring model of a flexible polymer chain. The normal and parallel components of the average end-to-end distance, mean radius of gyration and their distributions, the density profile, the force exerted on the slit walls, and the local bond orientation characteristics are obtained in slits of width D=4/10 (in units of the bead diameter) and for chain lengths N=50/300. We demonstrate that a wide range of static chain properties in normal direction can be described quantitatively by analytic model-independent expressions in perfect agreement with computer experiment. In particular, the observed profile of confinement-induced bond orientation is shown to closely match theory predictions. The anisotropy of confinement is found to be manifested most dramatically in the dynamic behavior of the polymer chain. We examine the relation between characteristic times for translational diffusion and lateral relaxation. It is demonstrated that the scaling predictions for lateral and normal relaxation times are in good agreement with our observations. A novel feature is the observed coupling of normal and lateral modes with two vastly different relaxation times. We show that the impact of grafting on lateral relaxation is equivalent to doubling the chain length.     

Self-assembly of patchy particles into polymer chains: a parameter-free comparison between Wertheim theory and Monte Carlo simulation

The authors numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear chains. The simplicity of the model allows for a close comparison, with no fitting parameters, between simulations and theoretical predictions based on the Wertheim perturbation theory. This comparison offers a unique framework for the analytic prediction of the properties of self-assembling particle systems in terms of molecular parameters and liquid state correlation functions. The Wertheim theory has not been previously subjected to stringent tests against simulation data for ordering across the polymerization transition. The authors numerically determine many of the thermodynamic properties governing this basic form of self-assembly (energy per particle, order parameter or average fraction of particles in the associated state, average chain length, chain length distribution, average end-to-end distance of the chains, and the static structure factor) and find that predictions of the Wertheim theory accord remarkably well with the simulation results.     

Simulation and model development for the equation of state of self assembling non-additive hard chain–hard monomer mixture

Molecular dynamics simulations for a short hard chain composed of a head and three tail groups interacting with non-additive size interactions with a hard sphere solvent were performed. Different densities and non-additivities were used. The equation of state for this mixture was investigated and models based on the first-order thermodynamic perturbation theory (TPT1) and the polymeric analog of the Percus–Yevick approximation (PPY) were developed to predict the compressibility factor of the mixture. The models predicted the compressibilities of the mixtures accurately at zero and negative non-additivities. However, at positive non-additivities, the models overpredicted the compressibilities especially at high densities. The TPT1 model was generally more accurate in predicting the compressibility factor than the PPY model. Microphase separation was observed at high densities and positive non-additivities.     

Density and chain conformation profiles of square-well chains confined in a slit by density-functional theory

Density and chain conformation profiles of square-well chains between two parallel walls were studied by using density-functional theory. The free energy of square-well chains is separated into two contributions: the hard-sphere repulsion and the attraction. The Heaviside function is used as the weighting function for both of the two parts. The equation of state of Hu et al. is used to calculate the excess free energy of the repulsive part. The equation of state of statistical associating fluid theory for chain molecules with attractive potentials of variable range [A. Gil-Villegas et al. J. Chem. Phys. 106, 4168 (1997)] is used to calculate the excess free energy of the attractive part. Because the wall is inaccessible to a mass center of a longer chain, there exists a sharp fall in the distribution of end-to-end distance near the wall as the chain length increases. When the average density of the system is not too low, the prediction of this work is in good agreement with computer simulation results for the density profiles and the chain conformation over a wide range of chain length, temperature, and attraction strength of the walls. However, when the average density and the temperature are very low, the prediction deviates to a certain degree from the computer simulation results for molecules with long chain length. A more accurate functional approximation is needed.