Molecular Insights on Morphology, Composition, and Stability of Mixed Micelles Formed by Ionic Surfactant and Nonionic Block Copolymer in Water Using Coarse-Grained Molecular Dynamics Simulations.

The nanoscale association domains are the ultimate determinants of the macroscopic properties of complex fluids involving amphiphilic polymers and surfactants, and hence, it is foremost important to understand the role of polymer/surfactant concentration on these domains. We have used coarse-grained molecular dynamics simulations to investigate the effect of polymer/surfactant concentration on the morphology of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO, i.e., pluronics or poloxamers) block copolymer, and ionic surfactants sodium dodecyl sulfate (SDS), mixed micelles in aqueous solution. The proclivity of the surfactant to form the mixed micelles is also probed using umbrella sampling simulations. In this study, we observed that the core of the pluronic + SDS formed mixed micelles consists of PPO, the alkyl tail of SDS, and some water molecules, whereas the PEO, water, and sulfate headgroups of SDS form a shell, consistent with experimental observations. The micelles are spherical at high-pluronic/low-SDS compositions, ellipsoidal at high-SDS/low-pluronic compositions, and wormlike-cylindrical at high-pluronic/high-SDS compositions. The transitions in micelle morphology are governed by the solvent accessible surface area of mixed aggregates, electrostatic repulsion between SDS-headgroups, and dehydration of PEO and PPO segments. The free energy barrier for SDS escape is much higher in mixed micelles than in pure SDS micelles, indicating a stronger tendency for SDS to form pluronic-SDS mixed micelles.

Does freezing induce self-assembly of polymers? A molecular dynamics study.

This work investigates the freezing-induced self-assembly (FISA) of polyvinyl alcohol (PVA) and PVA-like polymers using molecular dynamics simulations. In particular, the effect of the degree of supercooling, degree of polymerization, polymer type, and initial local concentration on the FISA was studied. It was found that the preeminent factor responsible for FISA is not the diffusion of the polymers away from the nucleating ice front, but the increase in the polymer's local concentration upon freezing of the solvent (water). At a higher degree of supercooling, the polymers are engulfed by the growing ice front, impeding their diffusion into the supercooled solution and finally inhibiting their self-assembly. Conversely, at a relatively lower degree of supercooling, the rate of diffusion of the polymers into the supercooled solution is higher, which increases their local concentration and results in FISA. FISA was also observed to depend on the polymer-solvent interactions. Strongly favorable solute-solvent interactions hinder the self-assembly, whereas unfavorable solute-solvent interactions promote the self-assembly. The polymer and aggregate morphology were investigated using the radius of gyration, end-to-end distance, and asphericity analysis. This study brings molecular insights into the quintessential factors governing self-assembly via freezing of the solvent, which is a novel self-assembly technique especially suitable for biomedical applications.

Does supercooled water retain its universal nucleation behavior under shear at high pressure?

Understanding the nucleation of homogeneous flow systems at high pressures is vital in protein crystallization and cryopreservation, where high pressure prevents the freezing of biological samples. This study examines the behavior of ice nucleation under shear at various pressures and explores the universal nucleation behavior of the sheared systems applied to supercooled water at higher pressures. In this study, the nucleation rates for the TIP4P/Ice model via a seeding method based on extended classical nucleation theory (CNT) are computed at pressures of 1, 100, 500, 700, and 1000 bar and a constant temperature of 240 K. Using extended CNT with explicitly embodying the shear rate, we analyzed the dependence of pressure on the transport and thermodynamic properties. In line with previous studies, we observed that Δµliq-ice and viscosity decrease while diffusivity increases with an increase in pressure. Furthermore, we showed that the dependence of the nucleation rate on shear at higher pressure is non-monotonic, with the maximum at optimal shear rates between 107 and 108 s-1. Our results demonstrate a non-monotonic pressure dependence of the optimal shear rates, which could originate from a violation of the Stokes-Einstein relation.

Understanding the role of polymers on the nucleating behavior of water in dilute supercooled solutions.

Understanding the nucleation behavior of water in dilute polymeric solutions is quintessential for the development of suitable artificial ice recrystallization inhibition (IRI) agents. Although poly(vinyl alcohol) (PVA) is found to be one of the most potent biomimetic IRI agents, the molecular understanding of the nucleation behavior of water in the presence of PVA is still lacking. Here, we use molecular dynamics to elucidate the role of concentration, degree of supercooling, degree of polymerization, and amphiphilicity of PVA and PVA-like polymers on the homogeneous nucleation of water in dilute polymeric solutions using the seeding method. Using classical nucleation theory (CNT), our simulations indicate an increase in the chemical potential difference between ice and melt that favors ice nucleation. However, it also predicts a significant increase in the ice-melt interfacial energy that impedes nucleation. The relative increase in the interfacial energy dominates the increase in the chemical potential difference, which results in a decrease in the nucleation rate of water with an increase in the solute concentration. This study contradicts the previous simulation study that suggested the promotion of homogeneous ice nucleation by PVA and supports the experimental observations of the heterogeneous origins of ice nucleation. Our results also suggest the non-classical origins of ice nucleation in polymeric solutions and the limitation of the CNT in predicting heterogeneous ice nucleation in polymeric solutions.

The pressure induced phase diagram of double-layer ice under confinement: a first-principles study.

Here, we present double-layer ice confined within various carbon nanotubes (CNTs) using state-of-the-art pressure induced (-5 GPa to 5 GPa) dispersion corrected density functional theory (DFT) calculations. We find that the double-layer ice exhibits remarkably rich and diverse phase behaviors as a function of pressure with varying CNT diameters. The lattice cohesive energies for various pure double layer ice phases follow the order of hexagonal > pentagonal > square tube > hexagonal-close-packed (HCP) > square > buckled-rhombic (b-RH). The confinement width was found to play a crucial role in the square and square tube phases in the intermediate pressure range of about 0-1 GPa. Unlike the phase transition in pure bilayer ice structures, the relative enthalpies demonstrate that the pentagonal phase, rather than the hexagonal structure, is the most stable ice polymorph at ambient pressure as well as in a deep negative pressure region, whereas the b-RH phase dominates under high pressure. The relatively short O⋯O distance of b-RH demonstrates the presence of a strong hydrogen bonding network, which is responsible for stabilizing the system.

Universal Nucleation Behavior of Sheared Systems.

Using molecular simulations and a modified classical nucleation theory, we study the nucleation, under flow, of a variety of liquids: different water models, Lennard-Jones, and hard sphere colloids. Our approach enables us to analyze a wide range of shear rates inaccessible to brute-force simulations. Our results reveal that the variation of the nucleation rate with shear is universal. A simplified version of the theory successfully captures the nonmonotonic temperature dependence of the nucleation behavior, which is shown to originate from the violation of the Stokes-Einstein relation.

Phase Behavior of Pure PSPC and PEGylated Multicomponent Lipid and Their Interaction with Paclitaxel: An All-Atom MD Study.

Exploring structural behavior of pure 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine (PSPC) and multicomponent PSPC and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N[amino(poly(ethylene glycol))-2000] (DSPE-PEG2000) membranes and their interaction with pharmaceutically important drugs carry huge importance in drug delivery. Using all-atom molecular dynamics (MD) simulations, we investigated the phase behavior of pure and PEGylated membranes at the temperature range of 280-360 K. We observe a gel-to-liquid crystalline phase transition for pure PSPC between 320 and 330 K, and in the case of multicomponent membranes, at 320 K, a coexistence of order-disorder phases is observed, which gradually transform to a complete liquid crystalline to gel phase between 320 and 310 K. We further studied the interaction of Paclitaxel with pure PSPC and PEGylated bilayers and elucidated the interaction behavior of Paclitaxel at the bilayer interfaces. Understanding of structural and interaction behaviors of the PEGylated bilayers with Paclitaxel will help to explore Paclitaxel-based drug applications in the future.

Building Unit Extractor for Metal-Organic Frameworks.

Metal-organic frameworks (MOFs) have relevance in extensive applications such as gas adsorption, separation, and energy storage. The tunability demonstrated by MOFs has encouraged research on MOF database generation via distinct methodologies. One of the crucial stages of these procedures is pre-processing, which often includes extraction of the building units (BUs). The process of BU extraction is intricate, and it is further amplified with the presence of solvent molecules/ions in the structure. This work presents MOF BU developer (mBUD), a platform to deconstruct the BUs, such as metal nodes, organic linkers, and functional groups of the MOF structure. The deconstruction algorithm has been assessed on the MOF structures of the CoRE MOF 2019 database. A total of 2,580 BUs have been extracted and provided as a database. This platform has been utilized to create a ready-to-use database of unique BUs deconstructed from the CoRE MOF database. We have also provided the web version of mBUD that can be easily used to extract BUs. These BUs can be employed to develop hypothetical MOF structures. It is envisaged that the BU database built with the deconstruction platform will aid the design of novel application-specific MOFs.

Homogeneous nucleation of sheared liquids: advances and insights from simulations and theory.

One of the most ubiquitous and technologically important phenomena in nature is the nucleation of homogeneous flowing systems. The microscopic effects of shear on a nucleating system are still imperfectly understood, although in recent years a consistent picture has emerged. The opposing effects of shear can be split into two major contributions for simple atomic and molecular liquids: increase of the energetic cost of nucleation, and enhancement of the kinetics. In this perspective, we describe the latest computational and theoretical techniques which have been developed over the past two decades. We collate and unify the overarching influences of shear, temperature, and supersaturation on the process of homogeneous nucleation. Experimental techniques and capabilities are discussed, against the backdrop of results from simulations and theory. Although we primarily focus on simple systems, we also touch upon the sheared nucleation of more complex systems, including glasses and polymer melts. We speculate on the promising directions and possible advances that could come to fruition in the future.

A hybrid topological and shape-matching approach for structure analysis.

Properties of crystalline and amorphous materials are characterized by the underlying long-range and local crystalline order. Deformations and defects are structural hallmarks of plasticity, ice formation, and crystal growth mechanisms. Partitioning topological networks into constituent crystal building blocks, which is the basis of topological identification criteria, is an intuitive approach for classification in both bulk and confinement. However, techniques reliant on the convex hull for assigning orientations of component units fail for non-convex blocks. Here, we propose a new framework, called Topological Unit Matching (TUM), which exploits information from topological criteria for an efficient shape-matching procedure. TUM is a general family of algorithms, capable of quantifying deformations and unambiguously determining grains of bulk and confined ice polymorphs. We show that TUM significantly improves the identification of quasi-one-dimensional ice by including deformed prism blocks. We demonstrate the efficacy of TUM by analyzing supercooled water nanoparticles, amorphous ice, and phase transitions in an ice nanotube. We also illustrate the superiority of TUM in resolving topological defect structures with minimal parameterization.

Effects of interfaces on structure and dynamics of water droplets on a graphene surface: A molecular dynamics study.

The structure and dynamics of water droplets on a bilayer graphene surface are investigated using molecular dynamics simulations. The effects of solid/water and air/water interfaces on the local structure of water droplets are analyzed in terms of the hydrogen bond distribution and tetrahedral order parameter. It is found that the local structure in the core region of a water droplet is similar to that in liquid water. On the other hand, the local structure of water molecules at the solid/water and air/water interfaces, referred to as the interface and surface regions, respectively, consists mainly of three-coordinated molecules that are greatly distorted from a tetrahedral structure. This study reveals that the dynamics in different regions of the water droplets affects the intermolecular vibrational density of states: It is found that in the surface and interface regions, the intensity of vibrational density of states at ∼50 cm-1 is enhanced, whereas those at ∼200 and ∼500 cm-1 are weakened and redshifted. These changes are attributed to the increase in the number of molecules having fewer hydrogen bonds in the interface and surface regions. Both single-molecule and collective orientation relaxations are also examined. Single-molecule orientation relaxation is found to be marginally slower than that in liquid water. On the other hand, the collective orientation relaxation of water droplets is found to be significantly faster than that of liquid water because of the destructive correlation of dipole moments in the droplets. The negative correlation between distinct dipole moments also yields a blueshifted libration peak in the absorption spectrum. It is also found that the water-graphene interaction affects the structure and dynamics of the water droplets, such as the local water structure, collective orientation relaxation, and the correlation between dipole moments. This study reveals that the water/solid and water/air interfaces strongly affect the structure and intermolecular dynamics of water droplets and suggests that the intermolecular dynamics, such as energy relaxation dynamics, in other systems with interfaces are different from those in liquid water.

d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations.

Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, determined using appropriate structural analysis techniques. We present d-SEAMS, a free and open-source postprocessing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures in both strong-confinement and bulk systems. For the first time, recent algorithms for confined ice structure determination have been implemented, along with topological network criteria for bulk ice structure determination. We also propose and validate a new order parameter for identifying the building blocks of quasi-one-dimensional ice. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture built with nix and employing a YAML-Lua scripting pipeline. The software has been designed to be user-friendly and extensible. The engine outputs are compatible with popular graphics software suites, allowing for immediate visual insights into the systems studied. We demonstrate the features of d-SEAMS by using it to analyze nucleation in the bulk regime and for quasi-one- and quasi-two-dimensional systems. Structural time evolution and quantitative metrics are determined for heterogeneous ice nucleation on a silver-exposed ß-AgI surface, homogeneous ice nucleation, flat monolayer square ice formation, and freezing of an ice nanotube.

A general topological network criterion for exploring the structure of icy nanoribbons and monolayers.

We develop intuitive metrics for quantifying complex nucleating systems under confinement. These are shown to arise naturally from the analysis of the topological ring network, and are amenable for use as order parameters for such systems. Drawing inspiration from qualitative visual inspection, we introduce a general topological criterion for elucidating the ordered structures of confined water, using a graph theoretic approach. Our criterion is based on primitive rings, and reinterprets the hydrogen-bond-network in terms of these primitives. This approach has no a priori assumptions, except the hydrogen bond definition, and may be used as an exploratory tool for the automated discovery of new ordered phases. We demonstrate the versatility of our criterion by applying it to analyse well-known monolayer ices. Our methodology is then extended to identify the building blocks of one-dimensional n-sided prismatic nanoribbon ices.

A simple molecular design for tunable two-dimensional imine covalent organic frameworks for optoelectronic applications.

Two-dimensional covalent organic frameworks (2D-COFs) belong to a new class of molecular materials that have attracted huge attention in recent years due to their analogous nature to graphene. In this work, we present a systematic study of the electronic structure, carrier mobility and work function of imine based 2D-COFs. We identify these 2D-COFs as a new class of semiconducting materials with tunable electronic/optoelectronic properties and significant mobility. The results show that by rationally doping 2D-COFs at the molecular level, it is possible to control their structural and optoelectronic responses. Cohesive energy calculations revealed that all the studied 2D-COFs are thermodynamically stable. Also, the calculated binding energy of 2D-COFs on HOPG was found to be less than 1 eV, which indicates that the COFs do not interact strongly with HOPG, and it will not affect their electronic properties. Additionally, we have synthesized a 2,4,6-pyrimidinetriamine based 2D-COF and experimentally measured its band gap using scanning tunnelling spectroscopy. The experimentally measured band gap is found to be in good agreement with theoretical results.

Seeding method for ice nucleation under shear.

Hydrodynamic flow can have complex and far-reaching consequences on the rate of homogeneous nucleation. We present a general formalism for calculating the nucleation rates of simply sheared systems. We have derived an extension to the conventional Classical Nucleation Theory, explicitly embodying the shear rate. Seeded molecular dynamics simulations form the backbone of our approach. The framework can be used for moderate supercooling, at which temperatures brute-force methods are practically infeasible. The competing energetic and kinetic effects of shear arise naturally from the equations. We show how the theory can be used to identify shear regimes of ice nucleation behavior for the mW water model, unifying disparate trends reported in the literature. At each temperature, we define a crossover shear rate in the limit of 1000 s-1-10 000 s-1, beyond which the nucleation rate increases steadily up to a maximum, at the optimal shear rate. For 235 K, 240 K, 255 K, and 260 K, the optimal shear rates are in the range of ≈106 s-1-107 s-1. For very high shear rates beyond 108 s-1, nucleation is strongly inhibited. Our results indicate that the optimal shear rates have a non-monotonic dependence on temperature.

Density Functional Theory Study of Aspirin Adsorption on BCN Sheets and their Hydrogen Evolution Reaction Activity: a Comparative Study with Graphene and Hexagonal Boron Nitride.

We explored the aspirin adsorption and their hydrogen evolution reaction (HER) activity in waste water of borocarbonitride sheets. Our results indicate that BCN sheets considered here show HER activity and exhibit superior performance regarding adsorption of aspirin in waste water in comparison with graphene and hexagonal boron nitride (h-BN). The drug molecule (aspirin) possesses a strong affinity to BCN, with the order of binding energy on following the order BCN∼h-BN>graphene. Upon drug adsorption, the band gap of h-BN is found to be reduced by up to 33 %, whereas the bandgaps of graphene and BCN remain unaltered that makes BCN a potential candidate for HER in waste water.

Evaporation induced self-assembly of different shapes and sizes of nanoparticles: A molecular dynamics study.

Molecular dynamics simulations of Lennard-Jones particles have been performed to study the self-assembled structure of nanoparticles (NPs) formed upon evaporation of nanofluid droplets on a heated surface. Different shapes of NPs such as a sphere, cube, triangle, and rod are considered in this work for the nanofluid. The influence of solvent-surface and NP-surface interaction strengths, size, and shape of NPs is analyzed on the structure of the NP deposit formed upon evaporation. The solvophilic substrate leads to the formation of different structures such as the hemispherical clump, monolayer, and ring depending on the size, shape, and interaction between other pairs of atoms. On the other hand, the solvophobic substrate always leads to a clump of NPs. Structural and thermodynamic properties are calculated to characterize the self-assembled structures. The low pair energy and high excess entropy are the characteristics of a ring structure. Furthermore, the mean square displacement of NPs is found to be lower for the ring structure compared to the hemispherical clump structure, and this observation is independent of the shape and size of the NP. The change in arrangement from disorder to order is observed for rod shaped NPs during evaporation.

An interaction potential to study the thermal structure evolution of a thermoelectric material: ß-Cu2 Se.

An interaction potential model has been developed, for the first time, for ß-Cu2 Se using the ab initio derived data. The structure and elastic constants of ß-Cu2 Se using the derived force-field are within a few percent of DFT derived structure and elastic constants and reported experimental structure. The derived force-field also shows remarkable ability to reproduce temperature dependent behavior of the specific heat and thermal expansion coefficient. The thermal structure evolution of the ß-Cu2 Se is studied by performing the molecular dynamic simulations using the derived force-field. The simulation results demonstrate that the Cu ions moves around the equilibrium lattice position within the temperature range of 500-800 K. However, at a temperature > 800 K, the Cu ions starts diffusing within the material, while the Se ions remains in their lattice position. The evaluated thermodynamic properties such as free energy and excess entropy, show that the increased Cu-Se interaction with the temperature makes the system more thermodynamically stable. © 2017 Wiley Periodicals, Inc.

Janus Gold Nanoparticles from Nanodroplets of Alkyl Thiols: A Molecular Dynamics Study.

Janus particles provide an asymmetry in structure, which can impart diverse functionalities leading to immense importance in various applications, ranging from targeted delivery to interfacial phenomena, including catalysis, electronics, and optics. In this work, we present results of a molecular dynamics study of the growth mechanism of coating on gold nanoparticles (AuNPs) from droplets of n-alkyl thiols with different chain lengths (C5 and C11) and terminal groups (CH3 and COOH). The effect of chain lengths and functional groups on the formation of a monolayer of alkyl thiols on AuNPs is investigated. A two-step mechanism, initiated by the binding of the droplet to the nanoparticle surface with a time constant on the order of ∼1 ns, followed by the diffusion-driven growth with a larger time constant (on the order of 100 ns), is shown to capture the growth dynamics of the monolayer. It is observed that the time required for complete wetting increases with an increase in the chain length. Moreover, the monolayer formation is slowed down in the presence of carboxyl groups because of strong hydrogen bonding. The kinetics of the n-alkyl thiols coating on the nanoparticles is found to be independent of the droplet size but carboxyl-terminated thiols spread more with increasing droplet size. Furthermore, different time constants for different chains and functional groups yield Janus coating when two droplets of alkyl thiols with different terminal groups are allowed to form monolayers on the nanoparticle. The Janus balance (ß) for different combinations of alkyl thiols and nanoparticle sizes varies in the range of 0.42-0.71.

Removal of Pb(II) Ion Using PAMAM Dendrimer Grafted Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Study.

The dendrimer polyamidoamine (PAMAM) has been widely applied in environmental applications as adsorbents for wastewater treatment. In this work, molecular dynamics simulations are conducted to understand the effect of dendrimer grafted graphene and graphene oxide on the structural and dynamical properties of the Pb2+ ion. The adsorption capacity of the metal ion is improved significantly, over 60%, using carboxyl terminal groups of a dendrimer molecule grafted on a graphene oxide surface. We examine the self-diffusion coefficient and residence time of Pb2+ ion near graphene and graphene oxide surfaces grafted with PAMAM dendrimers using terminal groups, -COO- and -OH. Further, the potential of mean force is analyzed to understand the role of different surface groups in enhancing the adsorption of the metal ion.