Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces

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

Force Field for Tricalcium Silicate and Insight into Nanoscale Properties: Cleavage, Initial Hydration, and Adsorption of Organic Molecules

Improvements in the sustainability and durability of building materials depend on understanding interfacial properties of various mineral phases at the nanometer scale. Tricalcium silicate (C₃S) is the major constituent of cement clinker and we present and validate a force field for atomistic simulations that provides excellent agreement with available experimental data, including X-ray structures, cleavage energies, elastic moduli, and IR spectra. Using this model and available measurements, we quantify key surface and interface properties of the dry and superficially hydrated mineral. An extensive set of possible cleavage planes shows cleavage energies in a range of 1300 to 1600 mJ/m² that are consistent with the observation of faceted crystallites with an aspect ratio near one. Using pure and hydroxylated surface models that represent the first step in the hydration reaction, we examined the adsorption mechanism of several organic amines and alcohols at different temperatures. Strong attraction between −20 and −50 kcal/mol is found as a result of complexation of superficial calcium ions, electrostatic interactions, and hydrogen bonds on the ionic surface. Agglomeration of cleaved C₃S surfaces in the absence of organic molecules was found to recover less than half the original cleavage energy (∼450 mJ/m²) associated with reduced Coulomb interactions between reconstructed surfaces. Additional adsorption of organic compounds below monolayer coverage reduced the attraction between even surfaces to less than 5% of the original cleavage energy (∼50 mJ/m²) related to their action as spacers between cleaved surfaces and mitigation of local electric fields. Computed agglomeration energies for a series of adsorbed organic compounds correlate with the reduction in surface forces in the form of measured grinding efficiencies. The force field is extensible to other cement phases and compatible with many platforms for molecular simulations (PCFF, COMPASS, CHARMM, AMBER, OPLS-AA, CVFF)

Carbon Nanotube Dispersion in Solvents and Polymer Solutions: Mechanisms, Assembly, and Preferences

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), <i>N</i>,<i>N</i>-dimethylacetamide (DMAc), and <i>N</i>,<i>N</i>-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 <i>via</i> 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

Facet Recognition and Molecular Ordering of Ionic Liquids on Metal Surfaces

Ionic liquids are widely used as solvents and reaction media due to low volatility, stability up to high temperature, and large dipole moment. Emergent applications also aim at the anisotropic growth of metal nanostructures in ionic liquids through facet-selective interactions although the governing mechanisms remain poorly understood. We employed a combination of quantum mechanical and classical simulations to analyze the structure and energetics of the self-assembly of ionic liquids on metal surfaces from single ion pairs to multilayers, using the example of 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIM]­[ES]) on the crystallographic {111}, {100}, and {110} facets of gold. Adsorption is controlled by the interplay of soft epitaxy, ionic interactions, induced charges, and steric effects related to the geometry of the cation and anion. These factors lead to characteristic molecular patterns on individual surfaces. Binding energies are similar irrespective of surface coverage and only slightly increase from {111} to {100} and {110} surfaces due to stronger surface corrugation and higher induced charge. The results explain specific experimental observations and aid in understanding particle growth in ionic liquid media. A mechanistic hypothesis for the formation of anisotropic gold nanorods in the presence of silver ions is made, in which silver retards the growth along {100} and {110} facets through underpotential deposition

Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field

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 Structure–Property Relationships of Polyacrylonitrile/CNT Composites as a Function of Polymer Crystallinity and CNT Diameter

Polyacrylonitrile (PAN)/carbon nanotube (CNT) composites are used as precursors for ultrastrong and lightweight carbon fibers. However, insights into the structure at the nanoscale and the relationships to mechanical and thermal properties have remained difficult to obtain. In this study, molecular dynamics simulation with accurate potentials and available experimental data were used to describe the influence of different degrees of PAN preorientation and CNT diameter on the atomic-scale structure and properties of the composites. The inclusion of CNTs in the polymer matrix is favored for an intermediate degree of PAN orientation and small CNT diameter whereas high PAN crystallinity and larger CNT diameter disfavor CNT inclusion. The glass transition at the CNT/PAN interface involves the release of rotational degrees of freedom of the polymer backbone and increased mobility of the protruding nitrile side groups in contact with the carbon nanotubes. The glass-transition temperature of the composite increases in correlation with the amount of CNT/polymer interfacial area per unit volume, i.e., in the presence of CNTs, for higher CNT volume fraction,  and inversely with CNT diameter. The increase in glass-transition temperature upon CNT addition is larger for PAN of lower crystallinity than for PAN of higher crystallinity. Interfacial shear strengths of the composites are higher for CNTs of smaller diameter and for PAN with preorientation, in correlation with more favorable CNT inclusion energies. The lowest interfacial shear strength was observed in amorphous PAN for the same CNT diameter. PAN with ∼75% crystallinity exhibited hexagonal patterns of nitrile groups near and far from the CNT interface which could influence carbonization into regular graphitic structures. The results illustrate the feasibility of near-quantitative insights into macroscale properties of polymer/CNT composites from simulations of nanometer-scale composite domains. Guidance is most effective when key assumptions in experiment and simulation are closely aligned, such as exfoliation versus bundling of CNTs, size, type, potential defects of CNTs, and precise measures for polymer crystallinity

Understanding Chemical Bonding in Alloys and the Representation in Atomistic Simulations

Alloys are widely used in catalysts and structural materials. The nature of chemical bonding and the origin of alloy formation energies, defect energies, and interfacial properties have not been well understood to date but are critical to material performance. In this contribution, we explain the polar nature of chemical bonding and an implementation in classical and reactive atomistic simulations to understand such properties more quantitatively. Electronegativity differences between metal atoms lead to polar bonding, and exothermic alloy formation energies are related to charge transfer between the different elements. These differences can be quantified by atomic charges using pairwise charge increments, determined by matching the computed alloy formation energy to experimentally measured alloy formation energies using pair potentials for the pure metals. The polar character of alloys is comparable to organic molecules and partially ionic minerals, for example, AlNi and AlNi₃ alloys assume significant atomic charges of ±0.40<i>e</i> and +0.60<i>e</i>/–0.20<i>e</i>, respectively. The subsequent analysis of defect sites and defect energies using force-field-based calculations shows excellent agreement with calculations using density functional theory and embedded atom models (EAM). The formation of vacancy and antisite defects is characterized by a redistribution of charge in the first shell of neighbor atoms in the classical models whereby electroneutrality is maintained and charge increments correlate with differences in electronegativity. The proposed atomic charges represent internal dipole and multipole moments, consistent with existing definitions for organic and inorganic compounds and with the extended Born model (Heinz, H.; Suter, U. W. <i>J. Phys. Chem. B</i> <b>2004,</b> <i>108</i> (47), 18341–18352). The method can be applied to any alloy and has a reproducibility of ±10%. In contrast, quantum mechanical charge schemes remain associated with deviations exceeding ±100%. The atomic charges for alloys provide a simple initial measure for the internal electronic structure, surface adsorption of molecules, and reactivity in catalysis and corrosion. The models are compatible with the Interface force field (IFF), CHARMM, AMBER, OPLS-AA, PCFF, CVFF, and GROMOS for reliable atomistic simulations of alloys and their interfaces with minerals and electrolytes from the nanometer scale to the micrometer scale

A Rational Biomimetic Approach to Structure Defect Generation in Colloidal Nanocrystals

Controlling the morphology of nanocrystals (NCs) is of paramount importance for both fundamental studies and practical applications. The morphology of NCs is determined by the seed structure and the following facet growth. While means for directing facet formation in NC growth have been extensively studied, rational strategies for the production of NCs bearing structure defects in seeds have been much less explored. Here, we report mechanistic investigations of high density twin formation induced by specific peptides in platinum (Pt) NC growth, on the basis of which we derive principles that can serve as guidelines for the rational design of molecular surfactants to introduce high yield twinning in noble metal NC syntheses. Two synergistic factors are identified in producing twinned Pt NCs with the peptide: (1) the altered reduction kinetics and crystal growth pathway as a result of the complex formation between the histidine residue on the peptide and Pt ions, and (2) the preferential stabilization of {111} planes upon the formation of twinned seeds. We further apply the discovered principles to the design of small organic molecules bearing similar binding motifs as ligands/surfactants to create single and multiple twinned Pd and Rh NCs. Our studies demonstrate the rich information derived from biomimetic synthesis and the broad applicability of biomimetic principles to NC synthesis for diverse property tailoring

РП Спецсеминар Совр. проблемы биофизики, биологии и биотех-и 2015 с печатью

Silica nanostructures find applications in drug delivery, catalysis, and composites, however, understanding of the surface chemistry, aqueous interfaces, and biomolecule recognition remain difficult using current imaging techniques and spectroscopy. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields over the last 30 years and reduces uncertainties in computed interfacial properties relative to experiment from several 100% to less than 5%. In addition, a silica surface model database is introduced for the full range of variable surface chemistry and pH (Q², Q³, Q⁴ environments with adjustable degree of ionization) that have shown to determine selective molecular recognition. The force field enables accurate computational predictions of aqueous interfacial properties of all types of silica, which is substantiated by extensive comparisons to experimental measurements. The parameters are integrated into multiple force fields for broad applicability to biomolecules, polymers, and inorganic materials (AMBER, CHARMM, COMPASS, CVFF, PCFF, INTERFACE force fields). We also explain mechanistic details of molecular adsorption of water vapor, as well as significant variations in the amount and dissociation depth of superficial cations at silica–water interfaces that correlate with ζ-potential measurements and create a wide range of aqueous environments for adsorption and self-assembly of complex molecules. The systematic analysis of binding conformations and adsorption free energies of distinct peptides to silica surfaces will be reported separately in a companion paper. The models aid to understand and design silica nanomaterials in 3D atomic resolution and are extendable to chemical reactions

Prediction of Specific Biomolecule Adsorption on Silica Surfaces as a Function of pH and Particle Size

Silica nanostructures are biologically available and find wide applications for drug delivery, catalysts, separation processes, and composites. However, specific adsorption of biomolecules on silica surfaces and control in biomimetic synthesis remain largely unpredictable. In this contribution, the variability and control of peptide adsorption on silica nanoparticle surfaces are explained as a function of pH, particle diameter, and peptide electrostatic charge using molecular dynamics simulations with the CHARMM-INTERFACE force field. Adsorption free energies and specific binding residues are analyzed in molecular detail, providing experimentally elusive, atomic-level information on the complex dynamics of aqueous electric double layers in contact with biological molecules. Tunable contributions to adsorption are described in the context of specific silica surface chemistry, including ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects. Remarkable agreement is found for computed peptide binding as a function of pH and particle size with respect to experimental adsorption isotherms and ζ-potentials. Representative surface models were built using characterization of the silica surfaces by transmission electron microscopy (TEM), scanning electron microscopy (SEM), Brunauer–Emmett–Teller (BET), thermalgravimetric analysis (TGA), ζ-potential, and surface titration measurements. The results show that the recently introduced interatomic potentials (Emami et al. <i>Chem. Mater.</i> <b>2014</b>, <i>26</i>, 2647) enable computational screening of a limitless number of silica interfaces to predict the binding of drugs, cell receptors, polymers, surfactants, and gases under realistic solution conditions at the scale of 1 to 100 nm. The highly specific binding outcomes underline the significance of the surface chemistry, pH, and topography