Molecular Modeling of Matter: Impact and Prospects in Engineering

Accurate prediction of solvent flux in sub-1-nm slit-pore nanosheet membranes

Nanosheet-based membranes have shown enormous potential for energy-efficient molecular transport and separation applications, but designing these membranes for specific separations remains a great challenge due to the lack of good understanding of fluid transport mechanisms in complex nanochannels. We synthesized reduced MXene/graphene hetero-channel membranes with sub-1-nm pores for experimental measurements and theoretical modeling of their structures and fluid transport rates. Our experiments showed that upon complete rejection of salt and organic dyes, these membranes with subnanometer channels exhibit remarkably high solvent fluxes, and their solvent transport behavior is very different from their homo-structured counterparts. We proposed a subcontinuum flow model that enables accurate prediction of solvent flux in sub-1-nm slit-pore membranes by building a direct relationship between the solvent molecule-channel wall interaction and flux from the confined physical properties of a liquid and the structural parameters of the membranes. This work provides a basis for the rational design of nanosheet-based membranes for advanced separation and emerging nanofluidics.

Chitosan-Coated MIL-100(Fe) as an Anticancer Drug Carrier: Theoretical and Experimental Investigation

MIL-100(Fe) was synthesized under biofriendly conditions at room temperature and pressure using iron(II) chloride as the source of iron, and it was coated with chitosan (CS), a natural polysaccharide. In this study, we used a computational technique to predict the amount of drug loading in MIL-100(Fe) and MIL-100(Fe)/CS with molecular dynamics software LAMMPS. Powder X-ray diffraction analysis was conducted to characterize the chitosan-coated MIL-100(Fe) loaded with cyclophosphamide (MIL-100(Fe)/CS/CP). The drug loading and release processes were quantified using UV spectroscopy at 193 nm. The toxic effect of MIL-100(Fe)/CS/CP was determined on human breast cancer (MCF-7) cells. In vivo images and H&E analysis show inhibition properties of MIL-100(Fe)/CS/CP on tumor cells. The conducted research indicates that computational calculation provides a unique insight into the drug adsorption since a proper understanding of the atomic interaction of MIL-100(Fe)/CS with anticancer drugs is important for developing experimental investigations. The biocompatibility and anticancer properties of chitosan molecules enhanced the tumor inhibitory effect of the particles compared with the MIL-100(Fe)/CP and free cyclophosphamide treatments.

Molecular modelling of the thermophysical properties of fluids: expectations, limitations, gaps and opportunities

This manuscript provides an overview of the current state of the art in terms of the molecular modelling of the thermophysical properties of fluids. It is intended to manage the expectations and serve as guidance to practising physical chemists, chemical physicists and engineers in terms of the scope and accuracy of the more commonly available intermolecular potentials along with the peculiarities of the software and methods employed in molecular simulations while providing insights on the gaps and opportunities available in this field. The discussion is focused around case studies which showcase both the precision and the limitations of frequently used workflows.

Deriving force fields with a multiscale approach:from ab initio calculations to molecular-based equations of state

Using theoretical and computational tools for predicting thermophysical properties of fluid systems and the soft matter has always been of interest to the physical, chemical, and engineering sciences. And certainly, the ultimate goal is to be able to compute these macroscopic properties from first principle calculations beginning with the very atomic constitution of matter. In this work, Mie potential parameters were obtained through dimer interaction energy curves derived from ab initio calculations to represent methane and methane-substituted molecules in a spherical 1-site coarse-grained model. Bottom-up-based Mie potential parameters of this work were compared to top-down-based ones from the statistical associating fluid theory (SAFT) models for the calculation of thermodynamic properties and critical point by molecular dynamics simulations and SAFT-VR Mie equation of state. Results demonstrated that bottom-up-based Mie potential parameters when averaging the Mie potential parameters of a representative population of conformers provide values close to the top-down-based ones from SAFT models and predict well properties of tetrahedral molecules. This shows the level of consistency embedded in the SAFT-VR Mie family of models and confers a status of a purely predictive equation of state for SAFT-VR Mie when a reasonable model is considered to represent a molecule of interest.

Calculating diffusion coefficients from molecular dynamics simulations for foam extrusion modelling of polypropylene with CO2, N2 and ethanol

In foaming processes, the blowing agent has a significant influence on the material behaviour and the necessary processing parameters. Low-density polypropylene foam sheets are usually produced with aliphatic hydrocarbons or alkanes as physical blowing agent. Due to the necessary safety precautions and the environmental impact, there is great interest in using alternative blowing agents such as CO2. The sole use of CO2 often leads to corrugation, open cells or surface defects on the foam sheet and therefore requires modifications to the process technology. For this reason, blowing agent mixtures based on CO2 and organic solvents are used for the production of foam sheets. For developing a process model describing the melt flow in the extrusion die and the formation of cells, specific material data like diffusion coefficients are necessary. For CO2 and N2 as sole blowing agent, experimental data exist in the literature. Since no experimental data are available for co-blowing agents such as ethanol at elevated temperatures as they occur in the foam process, these data were calculated using molecular dynamics (MD) simulations. The benefit of MD simulations lies in their ability to reduce the experimental effort and, in particular, to provide data in cases where this data is not available through experimental measurements. The calculated diffusion coefficient values are compared to experimental data from the literature and presented for CO2, N2 and ethanol in polypropylene. The calculated diffusion coefficients of CO2 and N2 are compared with literature results and agree well with them. For the ethanol molecules, the diffusion coefficient is compared relative to the both aforementioned ones considered the larger size of the ethanol molecule compared to N2 and CO2. The results of the diffusion coefficients for ethanol are reasonable compared to the values found for the other two molecules.

Structural Analysis of Molecular Materials Using the Pair Distribution Function

This is a review of atomic pair distribution function (PDF) analysis as applied to the study of molecular materials. The PDF method is a powerful approach to study short- and intermediate-range order in materials on the nanoscale. It may be obtained from total scattering measurements using X-rays, neutrons, or electrons, and it provides structural details when defects, disorder, or structural ambiguities obscure their elucidation directly in reciprocal space. While its uses in the study of inorganic crystals, glasses, and nanomaterials have been recently highlighted, significant progress has also been made in its application to molecular materials such as carbons, pharmaceuticals, polymers, liquids, coordination compounds, composites, and more. Here, an overview of applications toward a wide variety of molecular compounds (organic and inorganic) and systems with molecular components is presented. We then present pedagogical descriptions and tips for further implementation. Successful utilization of the method requires an interdisciplinary consolidation of material preparation, high quality scattering experimentation, data processing, model formulation, and attentive scrutiny of the results. It is hoped that this article will provide a useful reference to practitioners for PDF applications in a wide realm of molecular sciences, and help new practitioners to get started with this technique.

A Review on the Hydrodynamics of Taylor Flow in Microchannels: Experimental and Computational Studies

Taylor flow is a strategy-aimed flow to transfer conventional single-phase into a more efficient two-phase flow resulting in an enhanced momentum/heat/mass transfer rate, as well as a multitude of other advantages. To date, Taylor flow has focused on the processes involving gas–liquid and liquid–liquid two-phase systems in microchannels over a wide range of applications in biomedical, pharmaceutical, industrial, and commercial sectors. Appropriately micro-structured design is, therefore, a key consideration for equipment dealing with transport phenomena. This review paper highlights the hydrodynamic aspects of gas–liquid and liquid–liquid two-phase flows in microchannels. It covers state-of-the-art experimental and numerical methods in the literature for analyzing and simulating slug flows in circular and non-circular microchannels. The review’s main objective is to identify the considerable opportunity for further development of microflows and provide suggestions for researchers in the field. Available correlations proposed for the transition of flow patterns are presented. A review of the literature of flow regime, slug length, and pressure drop is also carried out.

Optical Analysis of the Internal Void Structure in Polymer Membranes for Gas Separation

Global warming by greenhouse gas emissions is one of the main threats of our modern society, and efficient CO2 capture processes are needed to solve this problem. Membrane separation processes have been identified among the most promising technologies for CO2 capture, and these require the development of highly efficient membrane materials which, in turn, requires detailed understanding of their operation mechanism. In the last decades, molecular modeling studies have become an extremely powerful tool to understand and anticipate the gas transport properties of polymeric membranes. This work presents a study on the correlation of the structural features of different membrane materials, analyzed by means of molecular dynamics simulation, and their gas diffusivity/selectivity. We propose a simplified method to determine the void size distribution via an automatic image recognition tool, along with a consolidated Connolly probe sensing of space, without the need of demanding computational procedures. Based on a picture of the void shape and width, automatic image recognition tests the dimensions of the void elements, reducing them to ellipses. Comparison of the minor axis of the obtained ellipses with the diameters of the gases yields a qualitative estimation of non-accessible paths in the geometrical arrangement of polymeric chains. A second tool, the Connolly probe sensing of space, gives more details on the complexity of voids. The combination of the two proposed tools can be used for a qualitative and rapid screening of material models and for an estimation of the trend in their diffusivity selectivity. The main differences in the structural features of three different classes of polymers are investigated in this work (glassy polymers, superglassy perfluoropolymers and high free volume polymers of intrinsic microporosity), and the results show how the proposed computationally less demanding analysis can be linked with their selectivities.

Molecular insight into the formation of adsorption clusters based on the zeta isotherm

This work presents a series of molecular dynamics simulations of argon adsorption on a silicon substrate with different lattice orientations. From the simulation results, the density profiles are discussed and the amount of adsorbed particles is obtained at different pressures. It is found that the solid surface orientation has a great influence on the density distributions and atomic arrangements near the surface. With the collected data, the thermal constants derived from the expression of zeta adsorption isotherms are determined. The calculated isotherms agree well with the simulation results. Also, from a microscopic point of view, the molecular insights show that the structures of the adsorbates are present as clusters with different numbers of particles. The size of the clusters changes with pressure. At a relatively small pressure ratio, most of the clusters consist of a single molecule. As the pressure ratio increases, larger sized clusters appear, forming various cluster-types. The molecular cluster distributions are closely consistent with the basic approximation of the zeta adsorption isotherm. Furthermore, the surface adsorption sites determined from molecular dynamics simulation show good agreement with that predicted by the zeta isotherm model, which reaffirms the effectiveness of the theoretical model. When the isotherm is extended to a pressure ratio greater than unity, a finite amount of adsorption is predicted and the wetting conditions are obtained. Affected by the solid surface orientations, the pressure ratio at wetting for the silicon substrate with the (111) surface plane is larger than those of the (100) and (110) surfaces, indicating that a higher subcooling is required for the wetting transition.

GEMS-Pack: A Graphical User Interface for the Packmol Program

We present GEMS-Pack, a graphical user interface for Packmol. Since Packmol is largely used by the molecular simulation community, this work provides a complement to it, in the form of a user-friendly and efficient interface. A tool for number/volume/density calculation is provided to make needed calculations faster. Also, a visualization utility is included, which lets the users preview how their systems will look like even before running the packing procedure. This application does not modify the original Packmol code; it works in a complementary way, by generating the input script and running it through the system's terminal. This program is part of a development project and is intended to be further extended. Two examples are described in this paper to illustrate GEMS-Pack usage.

Chemical bond effects in classical site density functional theory of inhomogeneous molecular liquids

Intra-molecular interactions or chemical bonds represent one of the main distinguishing characteristics of molecular fluids. Development of accurate and practical methods to treat these effects is one of the long standing problems in classical site density functional theory (SDFT). One particular instance when these issues become particularly severe is the case of classical interaction potentials with auxiliary sites or dummy atoms. In this situation, current SDFT implementations, such as the three-dimensional reference interaction site model, lead to nonphysical results. We re-examine this issue in this work using our recent reformulation of SDFT (Valiev and Chuev, J. Stat. Mech.: Theory Exp. 2018, 093201). We put forward a simple practical solution to this problem and illustrate its utility for the case of spherical solutes in diatomic liquids.

First-Principles Modeling in Heterogeneous Electrocatalysis

The last decade has witnessed tremendous progress in the development of computer simulation based on quantum mechanical description of the interactions between electrons and between electrons and atomic nuclei with electrode potentials taken into account–promoting the possibility to model electrocatalytic reactions. The cornerstone of this development was laid by the widely used computational hydrogen electrode method which involves a posteriori correction of standard constant charge first principles studies in solvent environment. The description of this technique and its contribution to our effort to understand electrocatalytic reactions on the active sites of metal-based nanoparticles are reviewed. The pathways and energetics of the relevant elementary reactions are presented. We also discussed a recent attempt in the literature to account for the inflow and outflow of electrons from the electrode as electrochemical reactions proceed, which has been greatly assisted by the development of density functional theory within the grand canonical framework. Going beyond the computational hydrogen electrode method by explicit incorporation of electrode potential within the calculations permits access to more detailed insights without requiring extra computational burden.

Multiscale Materials Modeling in an Industrial Environment

In this review, we sketch the materials modeling process in industry. We show that predictive and fast modeling is a prerequisite for successful participation in research and development processes in the chemical industry. Stable and highly automated workflows suitable for handling complex systems are a must. In particular, we review approaches to build and parameterize soft matter systems. By satisfying these prerequisites, efficiency for the development of new materials can be significantly improved, as exemplified here for formulation polymer development. This is in fact in line with recent Materials Genome Initiative efforts sponsored by the US government. Valuable contributions to product development are possible today by combining existing modeling techniques in an intelligent fashion, provided modeling and experiment work hand in hand.

Surface photografting of acrylic acid on poly(dimethylsiloxane). Experimental and dissipative particle dynamics studies

This work includes both experimental and theoretical studies of the wetting property changes of water on a surface of poly(dimethylsiloxane) (PDMS) modified with different amounts of acrylic acid (AA). The default surface properties of PDMS were changed from hydrophobic to hydrophilic behavior which was characterized with contact angle measurements by two approaches: (i) experimental tests of samples subjected to a photografting polymerization procedure to obtain a functionalized surface and (ii) DPD (dissipative particle dynamics) simulations which also involve the calculation of sets of repulsive parameters determined following two methods: the use of the "Blends" module in the Materials Studio software and the calculation of cohesive energy density with molecular simulations. Changes of contact angle values observed from both experimental and numerical simulation results provide qualitative and quantitative information on the wetting behavior of photografted surfaces.

Fundamental studies of methyl iodide adsorption in DABCO impregnated activated carbons

Methyl iodide capture from a water vapor stream using 1,4-diazabicyclo[2.2.2]octane (DABCO)-impregnated activated carbons is, for the first time, fundamentally described here on the atomic level by means of both molecular dynamics and grand canonical Monte Carlo simulations. A molecular dynamics annealing strategy was adopted to mimic the DABCO experimental impregnation procedure in a selected slitlike carbon pore. Predictions, restricted to the micropore region, are made about the adsorption isotherms of methyl iodide, water, and nitrogen on both impregnated and bare activated carbon models. Experimental and simulated nitrogen adsorption isotherms are compared for the validation of the impregnation strategy. Selectivity analyses of the preferential adsorption toward methyl iodide over water are also reported. These simulated adsorption isotherms sum up to previous experimental studies to provide an enhanced picture for this adsorption system of widespread use at nuclear plant HVAC facilities for the capture of radioactive iodine compounds.

Mixing atoms and coarse-grained beads in modelling polymer melts

We present a simple hybrid model for macromolecules where the single molecules are modelled with both atoms and coarse-grained beads. We apply our approach to two different polymer melts, polystyrene and polyethylene, for which the coarse-grained potential has been developed using the iterative Boltzmann inversion procedure. Our results show that it is possible to couple the two potentials without modifying them and that the mixed model preserves the local and the global structure of the melts in each of the case presented. The degree of resolution present in each single molecule seems to not affect the robustness of the model. The mixed potential does not show any bias and no cluster of particles of different resolution has been observed.

SAFT-γ force field for the simulation of molecular fluids: 2. Coarse-grained models of greenhouse gases, refrigerants, and long alkanes

In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement refrigerant with promising properties. The description of the fluid-phase behavior and the prediction of the other thermophysical properties obtained by molecular simulation using our SAFT-γ CG Mie force fields are found to be of comparable quality (and sometimes superior) to that obtained using the more sophisticated all-atom (AA) and united-atom (UA) models commonly employed in the field. We should emphasize that though the focus of our current work is on simple homonuclear models, the SAFT-γ methodology is based on a group contribution methodology which is naturally suited to the development of more sophisticated heteronuclear models.

Local viscosity of a fluid confined in a narrow pore

In this paper, molecular dynamics simulations of a simple Lennard-Jones fluid confined in narrow slit pores and undergoing shear have been performed. The aim is to investigate the effects of density inhomogeneities at the fluid-solid interfaces on the shear viscosity profiles. It has been found that the local viscosity was varying strongly with the distance from the solid walls for both dilute and dense fluid states with oscillations correlated to the density ones. To describe the computed viscosity profiles, we propose a scheme that uses the local average density model, combined with an adequate weight function, for the configurational viscosity and a semiempirical model for the translational viscosity. It is shown that the proposed approach is able to provide viscosity profiles in good agreement with those coming from simulations for different pore widths and for different fluid states (dilute to dense).

Turn-directed folding dynamics of β-hairpin-forming de novo decapeptide Chignolin

Realistic mechanistic pictures of β-hairpin formation, offering valuable insights into some of the key early events in protein folding, are accessible through short designed polypeptides as they allow atomic-level scrutiny through simulations. Here, we present a detailed picture of the dynamics and mechanism of β-hairpin formation of Chignolin, a de novo decapeptide, using extensive, unbiased molecular dynamics simulations. The results provide clear evidence for turn-directed broken-zipper folding and reveal details of turn nucleation and cooperative progression of turn growth, hydrogen-bond formations, and eventual packing of the hydrophobic core. Further, we show that, rather than driving folding through hydrophobic collapse, cross-strand side-chain packing could in fact be rate-limiting as packing frustrations can delay formation of the native hydrophobic core prior to or during folding and even cause relatively long-living misfolded or partially folded states that may nucleate aggregative events in more complex situations. The results support the increasing evidence for turn-centric folding mechanisms for β-hairpin formation suggested recently for GB1 and Peptide 1 based on experiments and simulations but also point to the need for similar examinations of polypeptides with larger numbers of cross-strand hydrophobic residues.