Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, ...sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance
in silico
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This review covers biomolecular recognition mechanisms on inorganic surfaces at the 1 to 100 nm scale, predictions of materials performance in comparison to experiment, and computational methods. The discussion focuses on biological and organic interfaces of metals, semimetals, biominerals, oxides, and quantum dots.
Adsorption of biomolecules and polymers to inorganic nanostructures plays a major role in the design of novel materials and therapeutics. The behavior of flexible molecules on solid surfaces at a ...scale of 1-1000 nm remains difficult and expensive to monitor using current laboratory techniques, while playing a critical role in energy conversion and composite materials as well as in understanding the origin of diseases. Approaches to implement key surface features and pH in molecular models of solids are explained, and distinct mechanisms of peptide recognition on metal nanostructures, silica and apatite surfaces in solution are described as illustrative examples. The influence of surface energies, specific surface features and protonation states on the structure of aqueous interfaces and selective biomolecular adsorption is found to be critical, comparable to the well-known influence of the charge state and pH of proteins and surfactants on their conformations and assembly. The representation of such details in molecular models according to experimental data and available chemical knowledge enables accurate simulations of unknown complex interfaces in atomic resolution in quantitative agreement with independent experimental measurements. In this context, the benefits of a uniform force field for all material classes and of a mineral surface structure database are discussed.
The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in ...molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute-solvent system, the solute-solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution.
Assembly of two-dimensional (2D) molecular arrays on surfaces produces a wide range of architectural motifs exhibiting unique properties, but little attention has been given to the mechanism by which ...they nucleate. Using peptides selected for their binding affinity to molybdenum disulfide, we investigated nucleation of 2D arrays by molecularly resolved in situ atomic force microscopy and compared our results to molecular dynamics simulations. The arrays assembled one row at a time, and the nuclei were ordered from the earliest stages and formed without a free energy barrier or a critical size. The results verify long-standing but unproven predictions of classical nucleation theory in one dimension while revealing key interactions underlying 2D assembly.
Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. Associated complex interfaces and processes remain difficult to analyze at the 1 to 100 nm scale using ...current laboratory techniques, and prior apatite models for atomistic simulations have been limited in the representation of chemical bonding, surface chemistry, and interfacial interactions. In this contribution, an accurate force field along with pH-resolved surface models for hydroxyapatite is introduced to represent chemical bonding, structural, surface, interfacial, and mechanical properties in quantitative agreement with experiment. The accuracy is orders of magnitude higher in comparison to earlier models and facilitates quantitative monitoring of inorganic-biological assembly. The force field is integrated into the AMBER, CHARMM, CFF, CVFF, DREIDING, GROMACS, INTERFACE, OPLS-AA, and PCFF force fields to enable realistic simulations of apatite-biological systems of any composition and ionic strength. Specific properties that are reproduced well in comparison to experiment include lattice constants (<0.5% deviation), IR spectrum, cleavage energies, immersion energies in water (<5% deviation), and elastic constants (<10% deviation). Interactions between mineral, water, and organic compounds are represented by standard combination rules without additional adjustable parameters and shown to achieve quantitative precision. Surface models for common (001), (010), (020), and (101) facets and nanocrystals are introduced as a function of pH on the basis of extensive experimental data. New insights into surface and immersion energies, the structure of aqueous interfaces, density profiles, and superficial dissolution are described. Most notably, hydroxyapatite-water interfaces exhibit facet-specific and pH-specific density profiles. Water stabilizes (010) facets better than (001) facets in a pH range from 10 to 5, consistent with preferred nanocrystal shape and growth in the (001) direction observed in experiment. Towards lower pH values, increasing penetration of water into sub-surface layers is observed, water density profiles flatten, and superficial dissolution occurs. The force field and surface models can be applied to elucidate mechanisms of mineralization as well as specific binding and assembly of peptides, polymer, and drugs. Extensions to substituted and defective apatites as well as to other calcium phosphate phases are feasible.
Debundling and dispersion of carbon nanotubes (CNTs) in polymer solutions play a major role in the preparation of carbon nanofibers due to early effects on interfacial ordering and mechanical ...properties. A roadblock toward ultrastrong fibers is the difficulty to achieve homogeneous dispersions of CNTs in polyacrylonitrile (PAN) and poly(methyl methacrylate) (PMMA) precursor solutions in solvents such as dimethyl sulfoxide (DMSO), N,N-dimethylacetamide (DMAc), and N,N-dimethylformamide (DMF). In this contribution, molecular dynamics simulations with accurate interatomic potentials for graphitic materials that include virtual π electrons are reported to analyze the interaction of pristine single wall CNTs with the solvents and polymer solutions at 25 °C. The results explain the barriers toward dispersion of SWCNTs and quantify CNT-solvent, polymer-solvent, as well as CNT-polymer interactions in atomic detail. Debundling of CNTs is overall endothermic and unfavorable with dispersion energies of +20 to +30 mJ/m2 in the pure solvents, + 20 to +40 mJ/m2 in PAN solutions, and +20 to +60 mJ/m2 in PMMA solutions. Differences arise due to molecular geometry, polar, van der Waals, and CH-π interactions. Among the pure solvents, DMF restricts CNT dispersion less due to the planar geometry and stronger van der Waals interactions. PAN and PMMA interact favorably with the pure solvents with dissolution energies of −0.7 to −1.1 kcal per mole monomer and −1.5 to −2.2 kcal per mole monomer, respectively. Adsorption of PMMA onto CNTs is stronger than that of PAN in all solvents as the molecular geometry enables more van der Waals contacts between alkyl groups and the CNT surface. Polar side groups in both polymers prefer interactions with the polar solvents. Higher polymer concentrations in solution lead to polymer aggregation via alkyl groups and reduce adsorption onto CNTs. PAN and PMMA solutions in DMSO and dilute solutions in DMF support CNT dispersion more than other combinations whereby the polymers significantly adsorb onto CNTs in DMSO solution. The observations by molecular simulations are consistent with available experimental data and solubility parameters and aid in the design of carbon nanofibers. The methods can be applied to other multiphase graphitic materials.
High temperature properties of glasses can be simulated using BKS and Pedone potentials.Surface and adsorption properties can be simulated using the INTERFACE potential.Parameter development ...necessitates understanding of chemical bonding.Realistic representation of surface chemistry and pH allows predictions of binding of biomolecules, polymers, and drugs.Guidance in mechanisms of nucleation and crystal growth can be obtained.
Silicates, glasses, and oxides are widely used in everyday applications such as surfaces of cell phones and tablets as well as in nanostructured form for therapeutics, catalysts, and composites. Modeling of the inorganic⿿organic interfaces at the 1⿿100nm scale has recently become more viable as suitable force fields and molecular models including details of oxide surface chemistry and pH dependent ionization have been introduced. Here we describe computational models for glasses, silica, and common oxides for simulations at high temperatures and at room temperature, including necessary chemical specificity to analyze surfaces and organic interfaces. The bulk structure of glasses, surface chemistry and type of molecular interactions governing adsorption, as well as the feasible accuracy is illustrated by examples. Applications and opportunities of simulation methods are discussed.
Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure ...assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.
The complexity of the molecular recognition and assembly of biotic–abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory ...instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic–organic and inorganic–biomolecular interfaces. The parametrization builds on an in-depth understanding of physical–chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical–chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid–water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic–organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described.
Nanoscale biological assemblies exemplified by exosomes, endosomes and capsids, play crucial roles in all living systems. Supraparticles (SP) from inorganic nanoparticles (NPs) replicate structural ...characteristics of these bioassemblies, but it is unknown whether they can mimic their biochemical functions. Here, we show that chiral ZnS NPs self-assemble into 70-100 nm SPs that display sub-nanoscale porosity associated with interstitial spaces between constituent NPs. Similarly to photosynthetic bacterial organelles, these SPs can serve as photocatalysts, enantioselectively converting L- or D-tyrosine (Tyr) into dityrosine (diTyr). Experimental data and molecular dynamic simulations indicate that the chiral bias of the photocatalytic reaction is associated with the chiral environment of interstitial spaces and preferential partitioning of enantiomers into SPs, which can be further enhanced by co-assembling ZnS with Au NPs. Besides replicating a specific function of biological nanoassemblies, these findings establish a path to enantioselective oxidative coupling of phenols for biomedical and other needs.
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