Polarization at metal-biomolecular interfaces in solution

Quantitative measurement of cation-mediated adhesion of DNA to anionic surfaces

Anionic polyelectrolytes, such as DNA, are attracted to anionic surfaces in the presence of multivalent cations. A major barrier toward molecular-level understanding of these attractive interactions is the paucity of measurements of the binding strength. Here, atomic force microscopy-based single molecule force spectroscopy was used to quantify the binding free energy of double-stranded DNA to an anionic surface, with complementary density functional theory calculations of the binding energies of metal ion-ligand complexes. The results support both electrostatic attraction and ion-specific binding. Our study suggests that the correlated interactions between counterions are responsible for attraction between DNA and an anionic surface, but the strength of this attraction is modulated by the identity of the metal ion. We propose a mechanism in which the strength of metal-ligand binding, as well as the preference for particular binding sites, influence both the concentration dependence and the strength of the DNA-surface interactions.

DNA-Au (111) interactions and transverse charge transport properties for DNA-based electronic devices

DNA's charge transfer and self-assembly characteristics have made it a hallmark of molecular electronics for the past two decades. A fast and efficient charge transfer mechanism with programmable properties using DNA nanostructures is required for DNA-based nanoelectronic applications and devices. The ability to integrate DNA with inorganic substrates becomes critical in this process. Such integrations may affect the conformation of DNA, altering its charge transport properties. Thus, using molecular dynamics simulations and first-principles calculations in conjunction with Green's function approach, we explore the impact of the Au (111) substrate on the conformation of DNA and analyze its effect on the charge transport. Our results indicate that DNA sequence, leading to its molecular conformation on the Au substrate, is critical to engineer charge transport properties. We demonstrate that DNA fluctuates on a gold substrate, sampling various distinct conformations over time. The energy levels, spatial locations of molecular orbitals and the DNA/Au contact atoms can differ between these distinct conformations. Depending on the sequence, at the HOMO, the charge transmission differs up to 60 times between the top ten conformations. We demonstrate that the relative positions of the nucleobases are critical in determining the conformations and the coupling between orbitals. We anticipate that these results can be extended to other inorganic surfaces and pave the way for understanding DNA-inorganic interface interactions for future DNA-based electronic device applications.

Computer Simulation of the Interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals

A prominent feature of the SARS-CoV-2 virus is the presence of a large glycoprotein spike protruding from the virus envelope. The spike determines the interaction of the virus with the environment and the host. Here, we used an all-atom molecular dynamics simulation method to investigate the interaction of up- and down-conformations of the S1 subunit of the SARS-CoV-2 spike with the (100) surface of Au, Ag, and Cu. Our results revealed that the spike protein is adsorbed onto the surface of these metals, with Cu being the metal with the highest interaction with the spike. In our simulations, we considered the spike protein in both its up-conformation S^up (one receptor binding domain exposed) and down-conformation S^down (no exposed receptor binding domain). We found that the affinity of the metals for the up-conformation was higher than their affinity for the down-conformation. The structural changes in the spike in the up-conformation were also larger than the changes in the down-conformation. Comparing the present results for metals with those obtained in our previous MD simulations of S^up with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in S^up, larger than those obtained in our previous studies.

Protein adsorption on a nanoparticle with a nanostructured surface

In the present study, the adsorption of a protein on a nanoparticle with a nanostructured surface, which is created using successively patterned Gaussian pillars (GPs), is simulated by considering the charge regulation within the electrical double layer of a silica nanoparticle (NP). Namely, the mathematical models for the adsorption mechanism, such as classical Langmuir model, extended Langmuir model, and two-state model, are coupled with charge regulation model. By this means, size and pH variables are able to included to the calculations. Moreover, free space, surface curvature, and conformational changes are also taken into account. For systematic investigation, the solution's pH, surface charge density, initial protein concentration, electrostatic charge of the protein, and the diameter of the spherical NP are varied. As a result, the vital properties of a nanoparticle, such as protonation/deprotonation, polarization, topography, and morphology, are considered in the current simulations. The surface charge density and surface chemistry change with NP and GP sizes. The present results reveal that the protein adsorption on an NP with a smooth surface reaches a faster complete surface coverage than an NP with a nanostructured surface. Both states of conformational changes are also affected by the presence of the GP.

Multiscale Modeling of Bio-Nano Interactions of Zero-Valent Silver Nanoparticles

Understanding the specifics of interaction between the protein and nanomaterial is crucial for designing efficient, safe, and selective nanoplatforms, such as biosensor or nanocarrier systems. Routing experimental screening for the most suitable complementary pair of biomolecule and nanomaterial used in such nanoplatforms might be a resource-intensive task. While a range of computational tools are available for prescreening libraries of proteins for their interactions with small molecular ligands, choices for high-throughput screening of protein libraries for binding affinities to new and existing nanomaterials are very limited. In the current work, we present the results of the systematic computational study of interaction of various biomolecules with pristine zero-valent noble metal nanoparticles, namely, AgNPs, by using the UnitedAtom multiscale approach. A set of blood plasma and dietary proteins for which the interaction with AgNPs was described experimentally were examined computationally to evaluate the performance of the UnitedAtom method. A set of interfacial descriptors (log P^NM, adsorption affinities, and adsorption affinity ranking), which can characterize the relative hydrophobicity/hydrophilicity/lipophilicity of the nanosized silver and its ability to form bio(eco)corona, was evaluated for future use in nano-QSAR/QSPR studies.

In-depth theoretical understanding of the chemical interaction of aromatic compounds with a gold nanoparticle

The orientations of aromatic molecules at the surface of gold nanoparticles are probed and characterized by a combination of several topological analyses, energy decomposition analyses, and infrared spectroscopy.

The implication of adsorption preferences of ions and surfactants on the shape control of gold nanoparticles: a microscopic, atomistic perspective

Shape modulation of nanoparticles is crucial for their tailored applications; however, it depends on surfactants, ions, reactants, and other additives present in the growth solution. Here we dissect the role of surfactants, their counterions (halide ions), silver ions, and gold reactant in gold nanoparticle anisotropic growth using polarizable surfaces and nanoseed molecular dynamics simulation models. Our planar surface models predict a 14%-16% increment in cetyltrimethylammonium bromide (CTAB) coverage on Au(111) and Au(100) due to the surface polarization effect. The CTAB micelle adsorbs compactly similar to that observed on non-polarizable surfaces. The cetyltrimethylammonium chloride (CTAC) micelle remains in solution leaving the polarizable gold surfaces unprotected, similar to that observed with the non-polarizable surfaces, which favors isotropic growth. The cetyltrimethylammonium iodide (CTAI) micelle adsorbs with higher surface densities than CTAB on all the surfaces. The surface polarizable penta-twinned nanoseed model predicts the total surface coverage of the cetyltrimethylammonium cation (CTA⁺), Br^- and Ag⁺ to be around two times higher on the side as compared to the tip of the nanoseed, leading to a 2.6 times higher initial rate of adsorption of AuCl₂^- on the tip than on the side. Predicted CTA⁺ surface densities on the tip and the side of the nanoseed are consistent with experimental results. Our simulations explain the growth mechanism of anisotropic nanoparticles and the microscopic origin of their controlled shapes.

On the origin of controlled anisotropic growth of monodisperse gold nanobipyramids

We elucidate the crucial role of the cetyl trimethylammonium bromide (CTAB) surfactant in the anisotropic growth mechanism of gold nano-bipyramids, nano-objects with remarkable optical properties and high tunability. Atomistic molecular dynamics simulations predict different surface coverages of the CTAB (positively charged) heads and their (bromide) counterions as function of the gold exposed surfaces. High concentration of CTAB surfactant promotes formation of gold nanograins in solution that work as precursors for the smooth anisotropic growth of more elongated nano-bipyramidal objects. Nanobipyramids feature higher index facets with respect to nanorods, allowing higher CTAB coverages that stabilize their formation and leading to narrower inter-micelles channels that smooth down their anisotropic growth. Absorption spectroscopy and scanning electron microscopy confirmed the formation of nanograins and demonstrated the importance of surfactant concentration on driving the growth towards nano-bipyramids rather than nanorods. The outcome explains the formation of the monodisperse bipyramidal nano-objects, the origin of their controlled shapes and sizes along with their remarkable stability.

Highly Heterogeneous Polarization and Solvation of Gold Nanoparticles in Aqueous Electrolytes

The performance of gold nanoparticles (NPs) in applications depends critically on the structure of the NP-solvent interface, at which the electrostatic surface polarization is one of the key characteristics that affects hydration, ionic adsorption, and electrochemical reactions. Here, we demonstrate significant effects of explicit metal polarizability on the solvation and electrostatic properties of bare gold NPs in aqueous electrolyte solutions of sodium salts of various anions (Cl^-, BF₄^-, PF₆^-, nitrophenolate, and 3- and 4-valent hexacyanoferrate), using classical molecular dynamics simulations with a polarizable core-shell model for the gold atoms. We find considerable spatial heterogeneity of the polarization and electrostatic potentials on the NP surface, mediated by a highly facet-dependent structuring of the interfacial water molecules. Moreover, ion-specific, facet-dependent ion adsorption leads to considerable alterations of the interfacial polarization. Compared to nonpolarizable NPs, surface polarization modifies water local dipole densities only slightly but has substantial effects on the electrostatic surface potentials and leads to significant lateral redistributions of ions on the NP surface. Besides, interfacial polarization effects cancel out in the far field for monovalent ions but not for polyvalent ions, as anticipated from continuum "image-charge" concepts. Far-field effective Debye-Hückel surface potentials change accordingly in a valence-specific fashion. Hence, the explicit charge response of metal NPs is crucial for the accurate description and interpretation of interfacial electrostatics (e.g., for charge transfer and interfacial polarization in catalysis and electrochemistry).

Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition

Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from -86 to -6 kcal mol-1. The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS2-based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.

Dynamics of Neutral and Charged Nanodiamonds in Aqueous Media Confined between Gold Surfaces under Normal and Shear Loading

The dynamics of cubo-octahedral nanodiamonds (NDs) with three different surface treatments and confined in aqueous environments between gold surfaces under shear and normal loading conditions have been characterized via molecular dynamics (MD) simulations. The treatments consisted of carboxyl (-COO-) or amino (-NH3 +) groups attached to the NDs, producing either negatively or positively charged NDs, respectively, and hydrogen-terminated surfaces producing neutral NDs. Simulations were performed in the presence and absence of induced image charges to explore the impact of electrostatic interactions on friction and surface deformation. Significant deformation of the gold surfaces was observed for negatively charged NDs placed between gold surfaces under external loads that were sufficient to displace water from the contact. Rolling and relatively high friction levels were also observed for the negatively charged NDs under the same conditions. In contrast, the neutral and positively charged NDs exhibited sliding behavior with only minor deformation of the gold surfaces. The results suggest that the size of the surface functional group plays a major role in determining whether NDs slide or roll on solid contacts. Higher friction levels were also observed in conjunction with induced image charges in the gold contacts. The results demonstrate how surface functionalization and surface-induced charges can work in combination to profoundly influence tribological performance.

Giant thermal expansion of a two-dimensional supramolecular network triggered by alkyl chain motion

Thermal expansion, the response in shape, area or volume of a solid with heat, is usually large in molecular materials compared to their inorganic counterparts. Resulting from the intrinsic molecule flexibility, conformational changes or variable intermolecular interactions, the exact interplay between these mechanisms is however poorly understood down to the molecular level. Here, we investigate the structural variations of a two-dimensional supramolecular network on Au(111) consisting of shape persistent polyphenylene molecules equipped with peripheral dodecyl chains. By comparing high-resolution scanning probe microscopy and molecular dynamics simulations obtained at 5 and 300 K, we determine the thermal expansion coefficient of the assembly of 980 ± 110 × 10^-6 K^-1, twice larger than other molecular systems hitherto reported in the literature, and two orders of magnitude larger than conventional materials. This giant positive expansion originates from the increased mobility of the dodecyl chains with temperature that determine the intermolecular interactions and the network spacing.

Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au-S Bonds

The interaction of amino acids with metal electrodes plays a crucial role in bioelectrochemistry and the emerging field of bionanoelectronics. Here we present benchmark calculations of the adsorption structure and energy of all natural amino acids on Au(111) in vacuum using a van-der-Waals density functional (revPBE-vdW) that showed good performance on the S22 set of weakly bound dimers (mean relative unsigned error (MRUE) wrt CCSD(T)/CBS = 13.3%) and adsorption energies of small organic molecules on Au(111) (MRUE wrt experiment = 11.2%). The vdW-DF results are then used to assess the accuracy of a popular force field for Au-amino acid interactions, GolP-CHARMM, which explicitly describes image charge interactions via rigid-rod dipoles. We find that while the force field underestimates adsorption distances, it does reproduce the binding energy rather well (MRUE wrt revPBE-vdW = 11.3%) with the MRUE decreasing in the order Cys, Met > amines > aliphatic > carboxylic > aromatic. We also present a parametrization of the bonding interaction between sulfur-containing molecules and the Au(111) surface and report force field parameters that are compatible with GolP-CHARMM. We believe the vdW-DF calculations presented herein will provide useful reference data for further force field development, and that the new Au-S bonding parameters will enable improved simulations of proteins immobilized on Au-electrodes via S-linkages.

Interdependent Roles of Electrostatics and Surface Functionalization on the Adhesion Strengths of Nanodiamonds to Gold in Aqueous Environments Revealed by Molecular Dynamics Simulations

Molecular dynamics simulations demonstrate that adhesion strengths as a function of charge for aqueous nanodiamonds (NDs) interacting with a gold substrate result from an interdependence of electrostatics and surface functionalization. The simulations reveal a water layer containing Na⁺ counterions between a negative ND with surface -COO^- functional groups that is not present for a positively charged ND with -NH₃⁺ functional groups. The closer proximity of the positive ND to the gold surface and the lack of cancelation of electrostatic interactions due to counterions and the water layer lead to an electrostatic adhesion force for the positive ND that is nearly three times larger than that of the negative ND. Prior interpretations of experimental tribological studies of ND-gold systems suggested that electrostatics or surface functionalization could be responsible for observed adhesion strength differences. The present work demonstrates how these two effects work together in determining adhesion for this system.

Controlling Redox Enzyme Orientation at Planar Electrodes

Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.

Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential

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.

Molecular dynamics models for predicting the behavior of metallic nanostructures typically do not take into account polarization effects in metals. Here, the authors introduce a polarizable Lennard–Jones potential that provides quantitative insight into the role of induced charges at metal surfaces and related complex material interfaces.

Multiscale simulations of ligand adsorption and exchange on gold nanoparticles

Multiscale simulations of CTAB/PEG-SH ligand adsorption and exchange kinetics on gold nanoparticles.

Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations

We describe a strategy of integrating quantum mechanical (QM), hybrid quantum mechanical/molecular mechanical (QM/MM) and MM simulations to analyze the physical properties of a solid/water interface.

Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

The adsorption of three homo-tripeptides, HHH, YYY, and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations. We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tripeptide binding affinities at aqueous Au(111) to be YYY > HHH > SSS. This ranking differs with that obtained from existing experimental data which used surface-immobilized Au nanoparticles as the target substrate. The influence of Au facet on these experimental findings is then considered, via our binding strength predictions of the relevant amino acids at aqueous Au(111) and Au(100)(1 × 1). The Au(111) interface supports an amino acid ranking of Tyr > HisA ≃ HisH > Ser, matching that of the tripeptides on Au(111), while the ranking on Au(100) is HisA > Ser ≃ Tyr ≃ HisH, with only HisA showing non-negligible binding. The substantial reduction in Tyr amino acid affinity for Au(100) vs Au(111) offers one possible explanation for the experimentally observed weaker adsorption of YYY on the nanoparticle-immobilized substrate compared with HHH. In a separate set of simulations, we predict the structures of the adsorbed tripeptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data.

Modeling and simulation of protein-surface interactions: achievements and challenges

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Carbon Nanotube Based Groundwater Remediation: The Case of Trichloroethylene

Adsorption of chlorinated organic contaminants (COCs) on carbon nanotubes (CNTs) has been gaining ground as a remedial platform for groundwater treatment. Applications depend on our mechanistic understanding of COC adsorption on CNTs. This paper lays out the nature of competing interactions at play in hybrid, membrane, and pure CNT based systems and presents results with the perspective of existing gaps in design strategies. First, current remediation approaches to trichloroethylene (TCE), the most ubiquitous of the COCs, is presented along with examination of forces contributing to adsorption of analogous contaminants at the molecular level. Second, we present results on TCE adsorption and remediation on pure and hybrid CNT systems with a stress on the specific nature of substrate and molecular architecture that would contribute to competitive adsorption. The delineation of intermolecular interactions that contribute to efficient remediation is needed for custom, scalable field design of purification systems for a wide range of contaminants.

Understanding and Designing the Gold-Bio Interface: Insights from Simulations

Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.

Decaheme Cytochrome MtrF Adsorption and Electron Transfer on Gold Surface

Emergent electrical properties of multiheme cytochromes have promising applications. We performed hybrid simulations (molecular dynamics, free energy computation, and kinetic Monte Carlo) to study decaheme cytochrome, MtrF adsorption on an Au (111) surface in water and the electron transfer (ET) efficiency. Our results reveal that the gold surface's dehydration serves as a crucial driving force for protein adsorption due to large surface tension. The most possible adsorption orientation is with the ET terminal (heme5) approaching the gold surface, which yields a pathway for ET between the substrate and the aqueous environment. Upon adsorption, protein's secondary structures and central domains (II and IV) bonded with heme-residues remain relatively stable. MtrF surface mobility is dictated by thiol-gold interaction and strong binding between Au(111) and peptide aromatic groups. ET transfer rate across protein heme-network along the solvent-to-surface direction is slightly larger than that of the reverse direction, but lower than that of the solvation structure.

Force fields for simulating the interaction of surfaces with biological molecules

The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide-surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities

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.

Facet selectivity in gold binding peptides: exploiting interfacial water structure

Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide-surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.

The effect of surface topography on the micellisation of hexadecyltrimethylammonium chloride at the silicon-aqueous interface

Amphiphilic aggregation at solid-liquid interfaces can generate mesostructured micelles that can serve as soft templates. In this study we have simulated the self-assembly of hexadecyltrimethylammonium chloride (C16TAC) surfactants at the Si(1 0 0)- and Si(1 1 1)-aqueous interfaces. The surfactants are found to form semicylindrical micelles on Si(1 0 0) but hemispherical micelles on Si(1 1 1). This difference in micelle structure is shown to be a consequence of the starkly different surface topographies that result from the reconstruction of the two silicon surfaces, and reveals that micelle structure can be governed by epitaxial matching even with non-polar substrates.

Predicting supramolecular self-assembly on reconstructed metal surfaces

The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern.

The role of chemistry and pH of solid surfaces for specific adsorption of biomolecules in solution--accurate computational models and experiment

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.

Understanding the microscopic origin of gold nanoparticle anisotropic growth from molecular dynamics simulations

We use molecular dynamics simulations in order to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. We provide the first atomistic model of different surfaces on gold nanoparticles in a growing electrolyte solution, and we describe the interaction of the metal with the surfactants, namely, cetyltrimethylammonium bromide (CTAB) and the ions. An innovative aspect is the inclusion of the role of the surfactants, which are explicitly modeled. We find that on all the investigated surfaces, namely, (111), (110), and (100), CTAB forms a layer of distorted cylindrical micelles where channels among micelles provide direct ion access to the surface. In particular, we show how AuCl2(-) ions, which are found in the growth solution, can freely diffuse from the bulk solution to the gold surface. We also find that the (111) surface exhibits a higher CTAB packing density and a higher electrostatic potential. Both elements would favor the growth of gold nanoparticles along the (111) direction. These findings are in agreement with the growth mechanisms proposed by the experimental groups of Murphy and Mulvaney.

Tailoring molecular specificity toward a crystal facet: a lesson from biorecognition toward Pt{111}

Surfactants with preferential adsorption to certain crystal facets have been widely employed to manipulate morphologies of colloidal nanocrystals, while mechanisms regarding the origin of facet selectivity remain an enigma. Similar questions exist in biomimetic syntheses concerning biomolecular recognition to materials and crystal surfaces. Here we present mechanistic studies on the molecular origin of the recognition toward platinum {111} facet. By manipulating the conformations and chemical compositions of a platinum {111} facet specific peptide, phenylalanine is identified as the dominant motif to differentiate {111} from other facets. The discovered recognition motif is extended to convert nonspecific peptides into {111} specific peptides. Further extension of this mechanism allows the rational design of small organic molecules that demonstrate preferential adsorption to the {111} facets of both platinum and rhodium nanocrystals. This work represents an advance in understanding the organic-inorganic interfacial interactions in colloidal systems and paves the way to rational and predictable nanostructure modulations for many applications.

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.

Influence of the shape of nanostructured metal surfaces on adsorption of single peptide molecules in aqueous solution

Self-assembly and function of biologically modified metal nanostructures depend on surface-selective adsorption; however, the influence of the shape of metal surfaces on peptide adsorption mechanisms has been poorly understood. The adsorption of single peptide molecules in aqueous solution (Tyr(12) , Ser(12) , A3, Flg-Na(3) ) is investigated on even {111} surfaces, stepped surfaces, and a 2 nm cuboctahedral nanoparticle of gold using molecular dynamics simulation with the CHARMM-METAL force field. Strong and selective adsorption is found on even surfaces and the inner edges of stepped surfaces (-20 to -60 kcal/mol peptide) in contrast to weaker and less selective adsorption on small nanoparticles (-15 to -25 kcal/mol peptide). Binding and selectivity appear to be controlled by the size of surface features and the extent of co-ordination of epitaxial sites by polarizable atoms (N, O, C) along the peptide chain. The adsorption energy of a single peptide equals a fraction of the sum of the adsorption energies of individual amino acids that is characteristic of surface shape, epitaxial pattern, and conformation constraints (often β-strand and random coil). The proposed adsorption mechanism is supported and critically evaluated by earlier sequence data from phage display, dissociation constants of small proteins as a function of nanoparticle size, and observed shapes of peptide-stabilized nanoparticles. Understanding the interaction of single peptides with shaped metal surfaces is a key step towards control over self-organization of multiple peptides on shaped metal surfaces and the assembly of superstructures from nanostructures.

Effect of solid surface charge on the binding behaviour of a metal-binding peptide

Over the last decade, solid-binding peptides have been increasingly used as molecular building blocks coupling bio- and nanotechnology. Despite considerable research being invested in this field, the effects of many surface-related parameters that define the binding of peptide to solids are still unknown. In the quest to control biological molecules at solid interfaces and, thereby, tailoring the binding characteristics of the peptides, the use of surface charge of the solid surface may probably play an important role, which then can be used as a potential tuning parameter of peptide adsorption. Here, we report quantitative investigation on the viscoelastic properties and binding kinetics of an engineered gold-binding peptide, 3RGBP(1), adsorbed onto the gold surface at different surface charge densities. The experiments were performed in aqueous solutions using an electrochemical dissipative quartz crystal microbalance system. Hydrodynamic mass, hydration state and surface coverage of the adsorbed peptide films were determined as a function of surface charge density of the gold metal substrate. Under each charged condition, binding of 3rGBP(1) displayed quantitative differences in terms of adsorbed peptide amount, surface coverage ratio and hydration state. Based on the intrinsically disordered structure of the peptide, we propose a possible mechanism for binding of the peptide that can be used for tuning surface adsorption in further studies. Controlled alteration of peptide binding on solid surfaces, as shown here, may provide novel methods for surface functionalization used for bioenabled processing and fabrication of future micro- and nanodevices.