Adsorption of cationic multicharged surfactants at liquid–gas interface

We present the review of the existing methods for describing adsorption at fluid interfaces that may be applicable for multiple charge cationic surfactant structures of various architectures—multiheaded (e.g., dicephalic) structures and multimeric surfactants (e.g., dimeric (so-called gemini), trimeric, tetrameric, etc.). We discuss the role of the prefactor the in the Gibbs adsorption equation originating from the number of charges present in the adsorbed layer and the reasons for the deviation from its thermodynamic value. We present several models of adsorption that can be used to describe surface tension isotherms and appreciate the role of prof. Peter Kralchevski in their development. Application of molecular dynamics methods combined with the approach based on the thermodynamic models of multicharged surfactant adsorption may lead to an explanation of some experimentally observed phenomena and can provide the basis for the development of novel materials designated for a variety of applications.     

Computer simulation of polypeptide adsorption on model biomaterials

When biomaterials are inserted in a biological environment, for instance in a body implant, proteins do quickly adsorb on the exposed surface. Such process is of fundamental importance, since it directs the subsequent cell adhesion. Here we review recent advances in this field obtained with molecular simulations. While coarse-grained models can provide important general results, as it has long been recognized in polymer science, the hierarchical structure of a very complex copolymer such as a protein, together with the nature of the biomaterial surface suggest that atomistic models are better suited to investigate these phenomena. Thus, after briefly mentioning some common features of coarse-grained and atomistic force fields, we first discuss early theoretical and coarse-grained simulation results about protein adsorption, and then we highlight the main results recently obtained by us with atomistic models. In particular, we discuss some conformational and energetic aspects of the adsorption of protein fragments with different secondary structure on surfaces of different wettability, including hydrophobic graphite and hydrophilic poly(vinylalcohol). We also consider other features, such as the simulation of the materials wettability, the hydration of the adsorbed fragments, their kinetics of spreading, and the sequential adsorption of two protein fragments on top of each other, highlighting the results of general interest.     

气体在无定型聚异戊二烯中扩散的分子动力学模拟

采用分子动力学模拟方法研究了多个温度下氧气、氮气及甲烷在无定型顺式1,4-聚异戊二烯中的扩散系数。在模拟过程中,使用COMPASS力场作为分子力场。应用COMPASS力场的势能函数,聚合物的密度及玻璃化转变温度的计算结果与实验值有较好吻合。在278-378 K的温度范围内,通过3或1.5 ns时长的正则系综动力学模拟,计算了不同温度下氧气、氮气及甲烷的扩散系数。结果表明,根据爱因斯坦关系式计算得到的扩散系数与实验结果比较接近。对气体扩散系数与温度的关系进一步研究,发现在278-378 K温度范围内,甲烷的扩散系数随温度变化的半对数曲线图是非线性的,而氧气和氮气的扩散系数随温度变化的半对数曲线图是线性的。本文研究结果有助于理解温度对气体扩散的影响机制,并为高温下气体在天然橡胶中扩散系数的测定及天然橡胶热氧老化建模分析提供依据。     

Developing a coarse-grained force field for the diblock copolymer poly(styrene-b-butadiene) from atomistic simulation

We have developed a coarse-grained force field for the poly(styrene-b-butadiene) diblock copolymer. We describe the computational methods and discuss how they were applied to develop a coarse-grained force field for this diblock copolymer from the atomistic simulation. The new force field contains three different bonds, four angles, five dihedral angles, and three nonbonded terms. We successfully tested this coarse-grained model against the chain properties, including static and dynamic properties, derived from the atomistic simulation; the results suggest that the coarse-grained force field is an effective model.     

The structure of the electric double layer: Atomistic versus continuum approaches

This article reviews recent forays in theoretical modeling of the double layer structure at electrode/electrolyte interfaces by current atomistic and continuum approaches. We will briefly discuss progress in both approaches and present a perspective on how to better describe the electric double layer by combining the unique advantages of each method. First-principles atomistic approaches provide the most detailed insights into the electronic and geometric structure of electrode/electrolyte interfaces. However, they are numerically too demanding to allow for a systematic investigation of the electric double layers over a wide range of electrochemical conditions. Yet, they can provide valuable input for continuum approaches that can capture the influence of the electrochemical environment on a larger length and time scale due to their numerical efficiency. However, continuum approaches rely on reliable input parameters. Conversely, continuum methods can provide a preselection of interface structures and conditions to be further studied on the atomistic level.     

Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers

Advances in theory and methods are making it practical to consider fully first principles (de novo) predictions of structures, properties and processes for organic materials. However, despite the progress there remains an enormous challenge in bridging the vast range of distances and time scales between de novo atomistic simulations and the quantitative continuum models for the macroscopic systems essential in industrial design and operations. Recent advances relevant to such developments include: quantum chemistry including continuum solvation and force field embedding, de novo force fields to describe phase transitions, molecular dynamics (MD) including continuum solvent, non equilibrium MD for rheology and thermal conductivity and mesoscale simulations. To provide some flavor for the opportunities we will illustrate some of the progress and challenges by summarizing some recent developments in methods and their applications to polymers and biopolymers. Four different topics will be covered: (1) hierarchical modeling approach applied to modeling olfactory receptors, (2) stabilization of leucine zipper coils by introduction of trifluoroleucine, (3) modeling response of polymers sensors for electronic nose, and (4) diffusion of gases in amorphous polymers.     

Adsorbents and columns in analytical high-performance liquid chromatography: a perspective with regard to development and understanding

A brief historical survey is presented on the evaluation of silica adsorbents in analytical HPLC. The theory of analytical HPLC is mostly still being based on the height equivalent to a theoretical plate concept and the van Deemter equation that was derived from gas phase adsorption involving a linear adsorption isotherm and fast mass transfer kinetics. One can obviously wonder whether the use of the van Deemter equation is relevant and valid for the evaluation of the performance of HPLC systems, where most often the liquid solutes involve charged molecules in electrolytes and in very many cases the adsorbates are macromolecules having diffusion coefficients of small magnitude. Instead of the van Deemter equation, a multi-scale modelling approach that involves microscopic and macroscopic dynamic non-linear mass-transfer-rate models should be employed. Furthermore, advanced experimental methods for the characterisation of porous media and the distribution of the density of immobilised active sites (e.g., ligands) on surfaces as well as microscopic pore-network modelling and molecular dynamics modelling and simulation methods could be used for the design of novel adsorbents whose porous structures and immobilised active sites would provide effective mass transport and adsorption rates for realising efficient separations as well as high dynamic capacities when larger throughputs are required.     

Hydrodynamics from statistical mechanics: combined dynamical-NEMD and conditional sampling to relax an interface between two immiscible liquids

We present a method to study hydrodynamic phenomena from atomistic simulations. In statistical mechanics, these fields are computed as the ensemble average over the time dependent probability density function corresponding to the time evolution of an initial conditional probability density function consistent with some initial conditions. These initial conditions typically consist in constraints on some macroscopic fields, e.g. the density field. We show how these processes can be studied by combining the dynamical approach to non-equilibrium molecular dynamics with the restrained simulation approach. As an illustration of our method, we study the relaxation to the equilibrium of an interface between two immiscible liquids. We show that, at a variance with the local time average method, the standard atomistic approach used in this field, our method is able to produce (macroscopic) fields satisfying the symmetry conditions of the problem.     

Characterization and quantification of the role of coherence in ultrafast quantum biological experiments using quantum master equations,atomistic simulations,and quantum process tomography

Long-lived electronic coherences in various photosynthetic complexes at cryogenic and room temperature have generated vigorous efforts both in theory and experiment to understand their origins and explore their potential role to biological function. The ultrafast signals resulting from the experiments that show evidence for these coherences result from many contributions to the molecular polarization. Quantum process tomography (QPT) is a technique whose goal is that of obtaining the time-evolution of all the density matrix elements based on a designed set of experiments with different preparation and measurements. The QPT procedure was conceived in the context of quantum information processing to characterize and understand general quantum evolution of controllable quantum systems, for example while carrying out quantum computational tasks. We introduce our QPT method for ultrafast experiments, and as an illustrative example, apply it to a simulation of a two-chromophore subsystem of the Fenna-Matthews-Olson photosynthetic complex, which was recently shown to have long-lived quantum coherences. Our Fenna-Matthews-Olson model is constructed using an atomistic approach to extract relevant parameters for the simulation of photosynthetic complexes that consists of a quantum mechanics/molecular mechanics approach combined with molecular dynamics and the use of state-of-the-art quantum master equations. We provide a set of methods that allow for quantifying the role of quantum coherence, dephasing, relaxation and other elementary processes in energy transfer efficiency in photosynthetic complexes, based on the information obtained from the atomistic simulations, or, using QPT, directly from the experiment. The ultimate goal of the combination of this diverse set of methodologies is to provide a reliable way of quantifying the role of long-lived quantum coherences and obtain atomistic insight of their causes.     

Grand challenges in quantum‐classical modeling of molecule–surface interactions

A detailed understanding of the adsorption of small molecules or macromolecules to a materials surface is of importance, for example, in the context of material and biomaterial research. Classical atomistic simulations in principle provide microscopic insight in the complex entropic and enthalpic interplay at the interface. However, an application of classical atomistic simulation techniques to such interface systems is a nontrivial problem, mostly because commonly used force fields cannot be straightforwardly applied, as they are usually developed to reproduce bulk properties of either solids or liquids but not the interfacial region between two phases. Therefore, a dual‐scale modeling approach has often been the method of choice in the past, in which the classical force field is parameterized such that quantum chemical information on near‐surface conformations and adsorption energies is reproduced by the classical force field. We will discuss in this review the current state‐of‐the‐art of quantum‐classical modeling of molecule–surface interactions and outline the major challenges in this field. In this context, we will, among other things, lay emphasis on discussing ways to obtain representable force fields and propose systematic and system‐independent strategies to optimize the quantum‐classical fitting procedure. © 2013 Wiley Periodicals, Inc.     

ReaxFF reactive force field for the Y-doped BaZrO3 proton conductor with applications to diffusion rates for multigranular systems

Proton-conducting perovskites such as Y-doped BaZrO 3 (BYZ) are promising candidates as electrolytes for a proton ceramic fuel cell (PCFC) that might permit much lower temperatures (from 400 to 600 degrees C). However, these materials lead to relatively poor total conductivity ( approximately 10 (-4) S/cm) because of extremely high grain boundary resistance. In order to provide the basis for improving these materials, we developed the ReaxFF reactive force field to enable molecular dynamics (MD) simulations of proton diffusion in the bulk phase and across grain boundaries of BYZ. This allows us to elucidate the atomistic structural details underlying the origin of this poor grain boundary conductivity and how it is related to the orientation of the grains. The parameters in ReaxFF were based entirely on the results of quantum mechanics (QM) calculations for systems related to BYZ. We apply here the ReaxFF to describe the proton diffusion in crystalline BYZ and across grain boundaries in BYZ. The results are in excellent agreement with experiment, validating the use of ReaxFF for studying the transport properties of these membranes. Having atomistic structures for the grain boundaries from simulations that explain the overall effect of the grain boundaries on diffusion opens the door to in silico optimization of these materials. That is, we can now use theory and simulation to examine the effect of alloying on both the interfacial structures and on the overall diffusion. As an example, these calculations suggest that the reduced diffusion of protons across the grain boundary results from the increased average distances between oxygen atoms in the interface, which necessarily leads to larger barriers for proton hopping. Assuming that this is the critical issue in grain boundary diffusion, the performance of BYZ for multigranular systems might be improved using additives that would tend to precipitate to the grain boundary and which would tend to pull the oxygens atoms together. Possibilities might be to use a small amount of larger trivalent ions, such as La or Lu or of tetravalent ions such as Hf or Th. Since ReaxFF can also be used to describe the chemical processes on the anode and cathode and the migration of ions across the electrode-membrane interface, ReaxFF opens the door to the possibility of atomistic first principles predictions on models of a complete fuel cell.     

Grand canonical Monte Carlo simulation of argon adsorption at the surface of silica nanopores: effect of pore size, pore morphology, and surface roughness

Argon adsorption (77 K) in atomistic silica nanopores of various sizes and shapes has been studied by means of grand canonical Monte Carlo simulations (GCMC). We discuss the effects of confinement (pore size), pore morphology (ellipsoidal, hexagonal, constricted pore), and surface texture (rough/smooth) on the thickness variation of the adsorbed film with pressure onto the disordered inner surface of porous materials (usually called t-plot or t-curve). We show that no confinement effect occurs when the diameter of the regular cylindrical pore is larger than 10 nm. For pores smaller than 6 nm, we find that the film thickness increases as the pore size decreases. We show that the adsorption isotherm in the rough pore can be described as the sum of an adsorbed amount similar to that found for a smooth pore (of the same radius) and a constant contribution due to atoms "trapped" in the infractuosities of the rough surface which act as a microporous texture. Simulation snapshots for Ar adsorption in hexagonal and ellipsoidal smooth pores indicate that at low pressures the gas/adsorbate interface retains memory of the pore shape and becomes cylindrical prior to the capillary condensation of the fluid in the pore. The film thickness in the hexagonal pore is close to that obtained for a cylindrical pore having a similar dimension. By contrast, we find that the film thickness for an ellipsoidal pore is always larger than that for an equivalent cylindrical pore (having the same length and volume but a circular section). We show that this effect strengthens as the pore size decreases and/or the pore asymmetry increases. Ar adsorption in a cylindrical constricted pore shows that the presence of the narrower part considerably modifies the adsorption mechanism. Finally, we report GCMC simulations of Ar adsorption (77 K) on a plane silica reference substrate for different intermolecular potentials. We discuss the effect of the interaction on the shape of the adsorption isotherm and compare our results with experiments.     

Efficient parametrization of complex molecule–surface force fields

We present an efficient scheme for parametrizing complex molecule–surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules. © 2015 Wiley Periodicals, Inc.     

Coarse-grained nonequilibrium approach to the molecular modeling of permeation through microporous membranes

We present a modeling technique that combines a statistical-mechanical coarse-graining scheme with a nonequilibrium molecular simulation algorithm to provide an efficient simulation of steady-state permeation across a microporous material. The coarse-graining scheme is based on the mapping of an atomistic model to a lattice using multidimensional free-energy and transition-state calculations. The nonequilibrium simulation algorithm is a stochastic, lattice version of the recently developed atomistic dual-control-volume grand canonical molecular dynamics. We demonstrate the approach on a model of methane permeating through a bulk portion of siliceous zeolite ZK4 at 300 K under imposed fugacity differences. We predict the coarse-grained (cage-level) density profiles and observe the development of nonlinearities as the magnitude of the fugacity difference is increased. From the net flux of methane we also predict a mean permeability coefficient under the various conditions. The simulation results are obtained over time scales on the order of microseconds and length scales on the order of dozens of nanometers.     

Atomistic modeling of enantioselection in chromatography

A review of atomistic molecular modeling studies related to chromatographic separations of enantiomers is presented. Only those types of calculations where direct interactions between a selector and a selectand are involved are described in this review; omitted are regression models. An emphasis is placed on comparing methods used for sampling potential energy surfaces implementing different methodologies like quantum and molecular mechanics for energy calculations, and molecular dynamics and Monte Carlo sampling strategies for simulations. Type I-V chiral stationary phases and additives for capillary electrophoresis and ion-pair chromatography are covered in this review.     

A discrete interaction model/quantum mechanical method for simulating surface-enhanced Raman spectroscopy

We have derived and implemented analytical gradients for the discrete interaction model/quantum mechanics (DIM/QM) method. DIM/QM combines an atomistic electrodynamics model with time-dependent density functional theory and thus enables modeling of the optical properties for a molecule while taking into account the local environment of a nanoparticle's surface. The DIM/QM analytical gradients allow for geometry optimizations, vibrational frequencies, and Raman spectra to be simulated for molecules interacting with metal nanoparticles. We have simulated the surface-enhanced Raman scattering (SERS) spectra for pyridine adsorbed on different sites of icosahedral nanoparticles with diameters between 1 and 8 nm. To describe the adsorption of the pyridine molecule onto the metal surface, we have implemented a coordination-dependent force field to differentiate the various local surface environments. We find that the DIM/QM method predicts geometries and frequencies that are in good agreement with full QM simulations and experiments. For the simulated SERS spectra of pyridine, we find a significant dependence on the adsorption site and the size of the metal nanoparticle. This illustrates the importance of accounting for the local environment around the molecule. The Raman enhancement factors are shown to roughly mirror the magnitude of the nanoparticle's local field about the molecule. Because the simulated nanoparticles are small, the plasmon peaks are quite broad which results in weak local electric fields and thus modest Raman enhancement factors.