Thermodynamically Consistent Force Fields and Molecular Models for the Assembly of Inorganic, Organic, and Biological Hybrid Nanostructures

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

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

Synthesis of Toroidal Gold Nanoparticles Assisted by Soft Templates

A three-component system comprising surfactant molecules and molecularly cross-linked metal centers assembles into nanoring structures. The thickness of the nanorings is determined by the dimensions of the surfactant bilayer while the dimensions of the ring opening depend on and can be regulated by the concentrations of the participating species. Once formed, these organic-inorganic hybrids can be transformed, by air plasma treatment, into all-metal nanorings exhibiting strong adsorption in the near IR

Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption

Control over selective recognition of biomolecules on inorganic nanoparticles is a major challenge for the synthesis of new catalysts, functional carriers for therapeutics, and assembly of renewable biobased materials. We found low sequence similarity among sequences of peptides strongly attracted to amorphous silica nanoparticles of various size (15-450 nm) using combinatorial phage display methods. Characterization of the surface by acid base titrations and zeta potential measurements revealed that the acidity of the silica particles increased with larger particle size, corresponding to between 5% and 20% ionization of silanol groups at pH 7. The wide range of surface ionization results in the attraction of increasingly basic peptides to increasingly acidic nanoparticles, along with major changes in the aqueous interfacial layer as seen in molecular dynamics simulation. We identified the mechanism of peptide adsorption using binding assays, zeta potential measurements, IR spectra, and molecular simulations of the purified peptides (without phage) in contact with uniformly sized silica particles. Positively charged peptides are strongly attracted to anionic silica surfaces by ion pairing of protonated N-termini, Lys side chains, and Arg side chains with negatively charged siloxide groups. Further, attraction of the peptides to the surface involves hydrogen bonds between polar groups in the peptide with silanol and siloxide groups on the silica surface, as well as ion-dipole, dipole-dipole, and van-der-Waals interactions. Electrostatic attraction between peptides and particle surfaces is supported by neutralization of zeta potentials, an inverse correlation between the required peptide concentration for measurable adsorption and the peptide pI, and proximity of cationic groups to the surface in the computation. The importance of hydrogen bonds and polar interactions is supported by adsorption of noncationic peptides containing Ser, His, and Asp residues, including the formation of multilayers. We also demonstrate tuning of interfacial interactions using mutant peptides with an excellent correlation between adsorption measurements, zeta potentials, computed adsorption energies, and the proposed binding mechanism. Follow-on questions about the relation between peptide adsorption on silica nanoparticles and mineralization of silica from peptide-stabilized precursors are raised

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

Synthesis of Toroidal Gold Nanoparticles Assisted by Soft Templates

A three-component system comprising surfactant molecules and molecularly cross-linked metal centers assembles into nanoring structures. The thickness of the nanorings is determined by the dimensions of the surfactant bilayer while the dimensions of the ring opening depend on and can be regulated by the concentrations of the participating species. Once formed, these organic–inorganic hybrids can be transformed, by air plasma treatment, into all-metal nanorings exhibiting strong adsorption in the near IR

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

Chemistry of Aqueous Silica Nanoparticle Surfaces and the Mechanism of Selective Peptide Adsorption

Control over selective recognition of biomolecules on inorganic nanoparticles is a major challenge for the synthesis of new catalysts, functional carriers for therapeutics, and assembly of renewable biobased materials. We found low sequence similarity among sequences of peptides strongly attracted to amorphous silica nanoparticles of various size (15–450 nm) using combinatorial phage display methods. Characterization of the surface by acid base titrations and zeta potential measurements revealed that the acidity of the silica particles increased with larger particle size, corresponding to between 5% and 20% ionization of silanol groups at pH 7. The wide range of surface ionization results in the attraction of increasingly basic peptides to increasingly acidic nanoparticles, along with major changes in the aqueous interfacial layer as seen in molecular dynamics simulation. We identified the mechanism of peptide adsorption using binding assays, zeta potential measurements, IR spectra, and molecular simulations of the purified peptides (without phage) in contact with uniformly sized silica particles. Positively charged peptides are strongly attracted to anionic silica surfaces by ion pairing of protonated N-termini, Lys side chains, and Arg side chains with negatively charged siloxide groups. Further, attraction of the peptides to the surface involves hydrogen bonds between polar groups in the peptide with silanol and siloxide groups on the silica surface, as well as ion–dipole, dipole–dipole, and van-der-Waals interactions. Electrostatic attraction between peptides and particle surfaces is supported by neutralization of zeta potentials, an inverse correlation between the required peptide concentration for measurable adsorption and the peptide p<i>I</i>, and proximity of cationic groups to the surface in the computation. The importance of hydrogen bonds and polar interactions is supported by adsorption of noncationic peptides containing Ser, His, and Asp residues, including the formation of multilayers. We also demonstrate tuning of interfacial interactions using mutant peptides with an excellent correlation between adsorption measurements, zeta potentials, computed adsorption energies, and the proposed binding mechanism. Follow-on questions about the relation between peptide adsorption on silica nanoparticles and mineralization of silica from peptide-stabilized precursors are raised