Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold

Insights into the mechanism of peptide fibril growth on gold surface

Understanding the formation of β-fibrils over the gold surface is of paramount interest in nano-bio-medicinal Chemistry. The intricate mechanism of self-assembly of neurofibrillogenic peptides and their growth over the gold surface remains elusive, as experiments are limited in unveiling the microscopic dynamic details, in particular, at the early stage of the peptide aggregation. In this work, we carried out equilibrium molecular dynamics and enhanced sampling simulations to elucidate the underlying mechanism of the growth of an amyloid-forming sequence of tau fragments over the gold surface. Our results disclose that the collective intermolecular interactions between the peptide chains and peptides with the gold surface facilitate the peptide adsorption, followed by integration, finally leading to the fibril formation.

Pretreatment-free SERS sensing of microplastics using a self-attention-based neural network on hierarchically porous Ag foams

Low-cost detection systems are needed for the identification of microplastics (MPs) in environmental samples. However, their rapid identification is hindered by the need for complex isolation and pre-treatment methods. This study describes a comprehensive sensing platform to identify MPs in environmental samples without requiring independent separation or pre-treatment protocols. It leverages the physicochemical properties of macroporous-mesoporous silver (Ag) substrates templated with self-assembled polymeric micelles to concurrently separate and analyze multiple MP targets using surface-enhanced Raman spectroscopy (SERS). The hydrophobic layer on Ag aids in stabilizing the nanostructures in the environment and mitigates biofouling. To monitor complex samples with multiple MPs and to demultiplex numerous overlapping patterns, we develop a neural network (NN) algorithm called SpecATNet that employs a self-attention mechanism to resolve the complex dependencies and patterns in SERS data to identify six common types of MPs: polystyrene, polyethylene, polymethylmethacrylate, polytetrafluoroethylene, nylon, and polyethylene terephthalate. SpecATNet uses multi-label classification to analyze multi-component mixtures even in the presence of various interference agents. The combination of macroporous-mesoporous Ag substrates and self-attention-based NN technology holds potential to enable field monitoring of MPs by generating rich datasets that machines can interpret and analyze.

High-Throughput Computational Screening of Solid-Binding Peptides

Inspired by biomineralization, a naturally occurring, protein-facilitated process, solid-binding peptides (SBPs) have gained much attention for their potential to fabricate various shaped nanocrystals and hierarchical nanostructures. The advantage of SBPs over other traditionally used synthetic polymers or short ligands is their tunable interaction with the solid material surface via carefully programmed sequence and being solution-dependent simultaneously. However, designing a sequence with targeted binding affinity or selectivity often involves intensive processes such as phage display, and only a limited number of sequences can be identified. Other computational efforts have also been introduced, but the validation process remains prohibitively expensive once a suitable sequence has been identified. In this paper, we present a new model to rapidly estimate the binding free energy of any given sequence to a solid surface. We show how the overall binding of a polypeptide can be estimated from the free energy contribution of each residue based on the statistics of the thermodynamically stable structure ensemble. We validated our model using five silica-binding peptides of different binding affinities and lengths and showed that the model is accurate and robust across a wider range of chemistries and binding strengths. The computational cost of this method can be as low as 3% of the commonly used enhanced sampling scheme for similar studies and has a great potential to be used in high-throughput algorithms to obtain larger training data sets for machine learning SBP screening.

Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces

We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.

Label-Free SERS and MD Analysis of Biomarkers for Rapid Point-of-Care Sensors Detecting Head and Neck Cancer and Infections

For the progress of point-of-care medicine, where individual health status can be easily and quickly monitored using a handheld sensor, saliva serves as one of the best-suited body fluids thanks to its availability and abundance of physiological indicators. Salivary biomarkers, combined with rapid and highly sensitive detection tools, may pave the way to new real-time health monitoring and personalized preventative therapy branches using saliva as a target matrix. Saliva is increasing in importance in liquid biopsy, a non-invasive approach that helps physicians diagnose and characterize specific diseases in patients. Here, we propose a proof-of-concept study combining the unique specificity in biomolecular recognition provided by surface-enhanced Raman spectroscopy (SERS) in combination with molecular dynamics (MD) simulations, which give leave to explore the biomolecular absorption mechanism on nanoparticle surfaces, in order to verify the traceability of two validated salivary indicators, i.e., interleukin-8 (IL-8) and lysozyme (LYZ), implicated in oropharyngeal squamous cell carcinoma (OSCC) and oral infection. This strategy simultaneously assures the detection and interpretation of protein biomarkers in saliva, ultimately opening a new route for the evolution of fast and accurate point-of-care SERS-based sensors of interest in precision medicine diagnostics.

Thermodynamics of the physisorption of capping agents on silver nanoparticles

Nanoscale silver particles have growing applications in biomedical and other technologies due to their unique antibacterial, optical, and electrical properties. The preparation of metal nanoparticles requires the action of a capping agent, such as thiol-containing compounds, to provide colloidal stability, prevent agglomeration, stop uncontrolled growth, and attenuate oxidative damage. However, despite the extensive use of these thiol-based capping agents, the structure of the capping agent layers on the metal surface and the thermodynamics of the formation of these layers remains poorly understood. Here, we leverage molecular dynamics simulations and free energy calculation techniques, to study the behavior of citrate and four thiol-containing capping agents commonly used to protect silver nanoparticles from oxidation. We have studied the single-molecule adsorption of these capping agents to the metal-water interface, their coalescence into clusters, and the formation of complete monolayers covering the metal nanoparticle. At sufficiently high concentrations, we find that allylmercaptan, lipoic acid, and mercaptohexanol spontaneously self-assemble into ordered layers with the thiol group in contact with the metal surface. The high density and ordered structure is presumably responsible for their improved protective characteristics relative to the other compounds studied.

The role of protein corona on nanodrugs for organ-targeting and its prospects of application

Nowadays, nanodrugs become a hotspot in the high-end medical field. They have the ability to deliver drugs to reach their destination more effectively due to their unique properties and flexible functionalization. However, the fate of nanodrugs in vivo is not the same as those presented in vitro, which indeed influenced their therapeutic efficacy in vivo. When entering the biological organism, nanodrugs will first come into contact with biological fluids and then be covered by some biomacromolecules, especially proteins. The proteins adsorbed on the surface of nanodrugs are known as protein corona (PC), which causes the loss of prospective organ-targeting abilities. Fortunately, the reasonable utilization of PC may determine the organ-targeting efficiency of systemically administered nanodrugs based on the diverse expression of receptors on cells in different organs. In addition, the nanodrugs for local administration targeting diverse lesion sites will also form unique PC, which plays an important role in the therapeutic effect of nanodrugs. This article introduced the formation of PC on the surface of nanodrugs and summarized the recent studies about the roles of diversified proteins adsorbed on nanodrugs and relevant protein for organ-targeting receptor through different administration pathways, which may deepen our understanding of the role that PC played on organ-targeting and improve the therapeutic efficacy of nanodrugs to promote their clinical translation.

Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.

Molecular Driving Force for Facet Selectivity of Sequence-Defined Amphiphilic Peptoids at Au-Water Interfaces

Shape-controlled colloidal nanocrystal syntheses often require facet-selective solution-phase chemical additives to regulate surface free energy, atom addition/migration fluxes, or particle attachment rates. Because of their highly tunable properties and robustness to a wide range of experimental conditions, peptoids represent a very promising class of next-generation functional additives for control over nanocrystal growth. However, understanding the origin of facet selectivity at the molecular level is critical to generalizing their design. Herein we employ molecular dynamics simulations and biased sampling methods and report stronger selectivity to Au(111) than to Au(100) for Nce3Ncp6, a peptoid that has been shown to assist the formation of 5-fold twinned Au nanostars. We find that facet selectivity is achieved through synergistic effects of both peptoid-surface and solvent-surface interactions. Moreover, the amphiphilic nature of Nce3Ncp6 together with the order of peptoid-peptoid and peptoid-surface binding energies, that is, peptoid-Au(100) < peptoid-peptoid < peptoid-Au(111), further amplifies its distinct collective behavior on different Au surfaces. Our studies provide a fundamental understanding of the molecular origin of facet-selective adsorption and highlight the possibility of future designs and uses of sequence-defined peptoids for predictive syntheses of nanocrystals with designed shapes and properties.

Chemical and Biophysical Signatures of the Protein Corona in Nanomedicine

An inconvenient hurdle in the practice of nanomedicine is the protein corona, a spontaneous collection of biomolecular species by nanoparticles in living systems. The protein corona is dynamic in composition and may entail improved water suspendability and compromised delivery and targeting to the nanoparticles. How much of this nonspecific protein ensemble is determined by the chemistry of the nanoparticle core and its surface functionalization, and how much of this entity is dictated by the biological environments that vary spatiotemporally in vivo? How do we "live with" and exploit the protein corona without significantly sacrificing the efficacy of nanomedicines in diagnosing and curing human diseases? This article discusses the chemical and biophysical signatures of the protein corona and ponders challenges ahead for the field of nanomedicine.

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.

Predicting Biomolecule Adsorption on MoS2 Nanosheets with High Structural Fidelity

A new force field, MoSu-CHARMM, for the description of bio-interfacial structures at the aqueous MoS2 interface is developed, based on quantum chemical data. The force field describes non-covalent interactions between...

Tuning Materials-Binding Peptide Sequences toward Gold- and Silver-Binding Selectivity with Bayesian Optimization

Peptide sequence engineering can potentially deliver materials-selective binding capabilities, which would be highly attractive in numerous biotic and abiotic nanomaterials applications. However, the number of known materials-selective peptide sequences is small, and identification of new sequences is laborious and haphazard. Previous attempts have sought to use machine learning and other informatics approaches that rely on existing data sets to accelerate the discovery of materials-selective peptides, but too few materials-selective sequences are known to enable reliable prediction. Moreover, this knowledge base is expensive to expand. Here, we combine a comprehensive and integrated experimental and modeling effort and introduce a Bayesian Effective Search for Optimal Sequences (BESOS) approach to address this challenge. Through this combined approach, we significantly expand the data set of Au-selective peptide sequences and identify an additional Ag-selective peptide sequence. Analysis of the binding motifs for the Ag-binders offers a roadmap for future prediction with machine learning, which should guide identification of further Ag-selective sequences. These discoveries will enable wider and more versatile integration of Ag nanoparticles in biological platforms.

Effects of the Chemical and Structural Properties of Silane Monolayers on the Organization of Water Molecules and Ions at Interfaces, from Molecular Dynamics Simulations

Understanding the organization of the hydration layer at functionalized silica surfaces is relevant for a large range of biosensing applications or surface phenomena such as biomolecule adsorption. Silane monolayers are widely used to functionalize silica surfaces. Using molecular dynamics simulations, we have investigated the role of silane molecule head-group charge, alkyl chain length, and surface coverage in the structural organization and dynamic properties of Na⁺ ions, Cl^- ions, and water molecules at the interface. The silane molecules studied are 3-aminopropyldimethylethoxysilane, n-propyldimethylmethoxysilane, octadecyldimethylmethoxysilane, and (dimethylamino)dimethylsilylundecanoate. Our results suggest that the distribution of interfacial ions is sensitive to the 2D dispersion of the silane-charged head groups. Also, while charged silane monolayers show a strong orientation of interfacial water molecules, which leads to a rupture in the hydrogen bond network and disturbs their tetrahedral organization, the arrangement of water molecules at the interface with uncharged silane monolayers seems to be related to the surface roughness and to alkyl chain length. In line with these results, the diffusion of ions and water molecules is higher at the CH₃ long monolayer interface than at the CH₃ short monolayer interface and at the charged monolayer interfaces. Also, whatever the silane molecules studied, bulk properties are recovered around 0.7 nm above the interface. The interfacial water organization is known to impact biomolecule adsorption. Therefore, these results could further help in optimizing the functionalization layers to capture analytes.

A Bespoke Force Field To Describe Biomolecule Adsorption at the Aqueous Boron Nitride Interface

Reliable manipulation of the interface between 2D nanomaterials and biomolecules represents a current frontier in nanoscience. The ability to resolve the molecular-level structures of these biointerfaces would provide a fundamental data set that is needed to enable systematic and knowledge-based progress in this area. These structures are challenging to obtain via experiment alone, and molecular simulations offer a complementary approach to address this problem. Compared with graphene, the interface between hexagonal boron nitride (h-BN) and biomolecules is relatively understudied at present. While several force fields are currently available for modeling the h-BN/water interface, there is a lack of a suitable force field that can describe the interactions between h-BN, liquid water, and biomolecules. Here, we use density functional theory calculations to create a force field, BoNi-CHARMM, to describe biomolecular interactions at the aqueous h-BN interface. Verifying our force field presents an additional challenge, given the scarcity of available experimental data for these interfaces. We test our force field against experimental evidence regarding the water/surface contact angle and confirm that the force field provides experimentally consistent values. We also present preliminary data regarding predictions of the free energy of adsorption of a selection of amino acids at the aqueous h-BN interface, revealing arginine and tryptophan to be among the strongest binders. This force field provides an opportunity to initiate a systematic progression in our current understanding of how to capture the intermolecular interactions at the h-BN biointerface.

Nanoparticle Concentration vs Surface Area in the Interaction of Thiol-Containing Molecules: Toward a Rational Nanoarchitectural Design of Hybrid Materials

The effect of accounting for the total surface in the association of thiol-containing molecules to nanosilver was assessed using isothermal titration calorimetry, along with a new open access algorithm that calculates the total surface area for samples of different polydispersity. Further, we used advanced molecular dynamic calculations to explore the underlying mechanisms for the interaction of the studied molecules in the presence of a nanosilver surface in the form of flat surfaces or as three-dimensional pseudospherical nanostructures. Our data indicate that not only is the total surface area available for binding but also the supramolecular arrangements of the molecules in the near proximity of the nanosilver surface strongly affects the affinity of thiol-containing molecules to nanosilver surfaces.

Poly(vinyl alcohol) as a water protecting agent for silver nanoparticles: the role of polymer size and structure

Chemical modification of silver nanoparticles (AgNPs) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of the stabilizing mechanism of PVA are still poorly understood. To gain a better understanding of the role of PVA in water protecting effects for silver nanoparticles, we developed an atomistic model of a AgNP grafted with single-chain PVA of various lengths. Our model, designed for classical molecular dynamics (MD) simulations, approximates the AgNP as a quasi-spherical silver nanocrystal with 3.9 nm diameter and uses a united-atom representation for PVA with its polymer chain length varying from 220 up to 1540 repeating units. We found that PVA adsorbs onto the AgNP surface through multiple non-covalent interactions, among which non-covalent bonding of the hydroxyl groups plays a key role. The analysis of adsorption isotherms by using the Hill, Scatchard, and McGhee & von Hippel models exhibits evidence for positive binding cooperativity with the cooperativity parameter varying from 1.55 to 2.12. Our results indicate that the size of the PVA polymer rather than its structure plays a crucial role in providing water protecting effects for the AgNP core, varying from 40% up to 91%. The water-protecting efficiency was well approximated by the Langmuir-Freundlich equation, allowing us to predict that the saturated coverage of the nanoparticle of a given diameter of 3.9 nm should occur when the PVA molecular weight approaches 115 kDa, which corresponds to the number of vinyl alcohol monomers being equal to 3100 units.

Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials

Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic-inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface-biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule-surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide-surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.

Cofibrillization of Pathogenic and Functional Amyloid Proteins with Gold Nanoparticles against Amyloidogenesis

Biomimetic nanocomposites and scaffolds hold the key to a wide range of biomedical applications. Here we show, for the first time, a facile scheme of cofibrillizing pathogenic and functional amyloid fibrils via gold nanoparticles (AuNPs) and their applications against amyloidogenesis. This scheme was realized by β-sheet stacking between human islet amyloid polypeptide (IAPP) and the β-lactoglobulin "corona" of the AuNPs, as revealed by transmission electron microscopy, 3D atomic force microscopy, circular dichroism spectroscopy, and molecular dynamics simulations. The biomimetic AuNPs eliminated IAPP toxicity, enabled X-ray destruction of IAPP amyloids, and allowed dark-field imaging of pathogenic amyloids and their immunogenic response by human T cells. In addition to providing a viable new nanotechnology against amyloidogenesis, this study has implications for understanding the in vivo cross-talk between amyloid proteins of different pathologies.

Probing the modulated formation of gold nanoparticles-beta-lactoglobulin corona complexes and their applications

Understanding the interactions between proteins and nanoparticles (NPs) along with the underlying structural and dynamic information is of utmost importance to exploit nanotechnology for biomedical applications. Upon adsorption onto a NP surface, proteins form a well-organized layer, termed the corona, that dictates the identity of the NP-protein complex and governs its biological pathways. Given its high biological relevance, in-depth molecular investigations and applications of NPs-protein corona complexes are still scarce, especially since different proteins form unique corona patterns, making identification of the biomolecular motifs at the interface critical. In this work, we provide molecular insights and structural characterizations of the bio-nano interface of a popular food-based protein, namely bovine beta-lactoglobulin (β-LG), with gold nanoparticles (AuNPs) and report on our investigations of the formation of corona complexes by combined molecular simulations and complementary experiments. Two major binding sites in β-LG were identified as being driven by citrate-mediated electrostatic interactions, while the associated binding kinetics and conformational changes in the secondary structures were also characterized. More importantly, the superior stability of the corona led us to further explore its biomedical applications, such as in the smartphone-based point-of-care biosensing of Escherichia coli (E. coli) and in the computed tomography (CT) of the gastrointestinal (GI) tract through oral administration to probe GI tolerance and functions. Considering their biocompatibility, edible nature, and efficient excretion through defecation, AuNPs-β-LG corona complexes have shown promising perspectives for future in vitro and in vivo clinical settings.

Computational Insight into the Interaction of Cytochrome C with Wet and PVP-Coated Ag Surfaces

In this work, the adsorption of cytochrome C (CytC) on wet {100}, {111}, {110}, and {120} silver surfaces has been investigated by computational simulations. The effect of polyvinylpyrrolidone (PVP) coating has also been studied. The main results obtained can be summarized as follow: (a) CytC strongly interacts with wet bare high index facets, while the adsorption over the {100} surface is disfavored due to the strong water structuring at the surface; (b) a nonselective protein adsorption mechanism is highlighted; (c) the native structure of CytC is well preserved during adsorption; (d) the heme group of CytC is never found to interact directly with the surface; (e) the interactions with the PVP-capped {100} surface is weak and specific. These results can be exploited to better control biological responses at engineered nanosurface, allowing the development of improved diagnostic tools.

Generation of Subsurface Voids, Incubation Effect, and Formation of Nanoparticles in Short Pulse Laser Interactions with Bulk Metal Targets in Liquid: Molecular Dynamics Study

The ability of short pulse laser ablation in liquids to produce clean colloidal nanoparticles and unusual surface morphology has been employed in a broad range of practical applications. In this paper, we report the results of large-scale molecular dynamics simulations aimed at revealing the key processes that control the surface morphology and nanoparticle size distributions by pulsed laser ablation in liquids. The simulations of bulk Ag targets irradiated in water are performed with an advanced computational model combining a coarse-grained representation of liquid environment and an atomistic description of laser interaction with metal targets. For the irradiation conditions that correspond to the spallation regime in vacuum, the simulations predict that the water environment can prevent the complete separation of the spalled layer from the target, leading to the formation of large subsurface voids stabilized by rapid cooling and solidification. The subsequent irradiation of the laser-modified surface is found to result in a more efficient ablation and nanoparticle generation, thus suggesting the possibility of the incubation effect in multipulse laser ablation in liquids. The simulations performed at higher laser fluences that correspond to the phase explosion regime in vacuum reveal the accumulation of the ablation plume at the interface with the water environment and the formation of a hot metal layer. The water in contact with the metal layer is brought to the supercritical state and provides an environment suitable for nucleation and growth of small metal nanoparticles from metal atoms emitted from the hot metal layer. The metal layer itself has limited stability and can readily disintegrate into large (tens of nanometers) nanoparticles. The layer disintegration is facilitated by the Rayleigh-Taylor instability of the interface between the higher density metal layer decelerated by the pressure from the lighter supercritical water. The nanoparticles emerging from the layer disintegration are rapidly cooled and solidified due to the interaction with water environment, with a cooling rate of ∼2 × 10¹² K/s observed in the simulations. The computational prediction of two distinct mechanisms of nanoparticle formation yielding nanoparticles with different characteristic sizes provides a plausible explanation for the experimental observations of bimodal nanoparticle size distributions in laser ablation in liquids. The ultrahigh cooling and solidification rates suggest the possibility for generation of nanoparticles featuring metastable phases and highly nonequilibrium structures.

Unveiling the Molecular Structure of Pulmonary Surfactant Corona on Nanoparticles

The growing risk of human exposure to airborne nanoparticles (NPs) causes a general concern on the biosafety of nanotechnology. Inhaled NPs can deposit in the deep lung at which they interact with the pulmonary surfactant (PS). Despite the increasing study of nano-bio interactions, detailed molecular mechanisms by which inhaled NPs interact with the natural PS system remain unclear. Using coarse-grained molecular dynamics simulation, we studied the interaction between NPs and the PS system in the alveolar fluid. It was found that regardless of different physicochemical properties, upon contacting the PS, both silver and polystyrene NPs are immediately coated with a biomolecular corona that consists of both lipids and proteins. Structure and molecular conformation of the PS corona depend on the hydrophobicity of the pristine NPs. Quantitative analysis revealed that lipid composition of the corona formed on different NPs is relatively conserved and is similar to that of the bulk phase PS. However, relative abundance of the surfactant-associated proteins, SP-A, SP-B, and SP-C, is notably affected by the hydrophobicity of the NP. The PS corona provides the NPs with a physicochemical barrier against the environment, equalizes the hydrophobicity of the pristine NPs, and may enhance biorecognition of the NPs. These modifications in physicochemical properties may play a crucial role in affecting the biological identity of the NPs and hence alter their subsequent interactions with cells and other biological entities. Our results suggest that all studies of inhalation nanotoxicology or NP-based pulmonary drug delivery should consider the influence of the PS corona.

Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures

An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face challenges in their successful application to model the biotic-abiotic interface, related to several factors. For instance, simulations require a plausible description of the chemistry and the physics of the interface, which comprises two very different states of matter, in the presence of liquid water. Also, it is essential that the conformational ensemble be comprehensively characterized under these conditions; this is especially challenging because intrinsically disordered peptides do not typically admit one single structure or set of structures. Moreover, a plausible structural model of the substrate is required, which may require a high level of detail, even for single-element materials such as Au surfaces or graphene. Developing and applying strategies to make credible predictions of the conformational ensemble of adsorbed peptides and using these to construct structure-property relationships of these interfaces have been the goals of our efforts. We have made substantial progress in developing interatomic potentials for these interfaces and adapting advanced conformational sampling approaches for these purposes. This Account summarizes our progress in the development and deployment of interfacial force fields and molecular simulation techniques for the purpose of elucidating these insights at biomolecule-materials interfaces, using examples from our laboratories ranging from noble-metal interfaces to graphitic substrates (including carbon nanotubes and graphene) and oxide materials (such as titania). In addition to the well-established application areas of plasmonic materials, biosensing, and the production of medical implant materials, we outline new directions for this field that have the potential to bring new advances in areas such as energy materials and regenerative medicine.

NanoEHS beyond Toxicity - Focusing on Biocorona

The first phase of environmental health and safety of nanomaterials (nanoEHS) studies has been mainly focused on evidence-based investigations that probe the impact of nanoparticles, nanomaterials and nano-enabled products on biological and ecological systems. The integration of multiple disciplines, including colloidal science, nanomaterial science, chemistry, toxicology/immunology and environmental science, is necessary to understand the implications of nanotechnology for both human health and the environment. While strides have been made in connecting the physicochemical properties of nanomaterials with their hazard potential in tiered models, fundamental understanding of nano-biomolecular interactions and their implications for nanoEHS is largely absent from the literature. Research on nano-biomolecular interactions within the context of natural systems not only provides important clues for deciphering nanotoxicity and nanoparticle-induced pathology, but also presents vast new opportunities for screening beneficial material properties and designing greener products from bottom up. This review highlights new opportunities concerning nano-biomolecular interactions beyond the scope of toxicity.

Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

Plasmon-enhanced two-photon-induced isomerization for highly-localized light-based actuation of inorganic/organic interfaces

Two-photon initiated photo-isomerization of an azobenzene moiety adsorbed on silver nanoparticles (Ag NPs) is demonstrated. The azobenzene is linked to a materials-binding peptide that brings it into intimate contact with the Ag NP surface, producing a dramatic enhancement of its two-photon absorbance. An integrated modeling approach, combining advanced conformational sampling with Quantum Mechanics/Capacitance Molecular Mechanics and response theory, shows that charge transfer and image charges in the Ag NP generate local fields that enhance two-photon absorption of the cis isomer, but not the trans isomer, of adsorbed molecules. Moreover, dramatic local field enhancement is expected near the localized surface plasmon resonance (LSPR) wavelength, and the LSPR band of the Ag NPs overlaps the azobenzene absorbance that triggers cis to trans switching. As a result, the Ag NPs enable two-photon initiated cis to trans isomerization, but not trans to cis isomerization. Confocal anti-Stokes fluorescence imaging shows that this effect is not due to local heating, while the quadratic dependence of switching rate on laser intensity is consistent with a two-photon process. Highly localized two-photon initiated switching could allow local manipulation near the focal point of a laser within a 3D nanoparticle assembly, which cannot be achieved using linear optical processes.

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.

Optical Actuation of Inorganic/Organic Interfaces: Comparing Peptide-Azobenzene Ligand Reconfiguration on Gold and Silver Nanoparticles

Photoresponsive molecules that incorporate peptides capable of material-specific recognition provide a basis for biomolecule-mediated control of the nucleation, growth, organization, and activation of hybrid inorganic/organic nanostructures. These hybrid molecules interact with the inorganic surface through multiple noncovalent interactions which allow reconfiguration in response to optical stimuli. Here, we quantify the binding of azobenzene-peptide conjugates that exhibit optically triggered cis-trans isomerization on Ag surfaces and compare to their behavior on Au. These results demonstrate differences in binding and switching behavior between the Au and Ag surfaces. These molecules can also produce and stabilize Au and Ag nanoparticles in aqueous media where the biointerface can be reproducibly and reversibly switched by optically triggered azobenzene isomerization. Comparisons of switching rates and reversibility on the nanoparticles reveal differences that depend upon whether the azobenzene is attached at the peptide N- or C-terminus, its isomerization state, and the nanoparticle composition. Our integrated experimental and computational investigation shows that the number of ligand anchor sites strongly influences the nanoparticle size. As predicted by our molecular simulations, weaker contact between the hybrid biomolecules and the Ag surface, with fewer anchor residues compared with Au, gives rise to differences in switching kinetics on Ag versus Au. Our findings provide a pathway toward achieving new remotely actuatable nanomaterials for multiple applications from a single system, which remains difficult to achieve using conventional approaches.

New Insights into Peptide-Silver Nanoparticle Interaction: Deciphering the Role of Cysteine and Lysine in the Peptide Sequence

We studied the interaction of four new pentapeptides with spherical silver nanoparticles. Our findings indicate that the combination of the thiol in Cys and amines in Lys/Arg residues is critical to providing stable protection for the silver surface. Molecular simulation reveals the atomic scale interactions that underlie the observed stabilizing effect of these peptides, while yielding qualitative agreement with experiment for ranking the affinity of the four pentapeptides for the silver surface.

Toward a modular multi-material nanoparticle synthesis and assembly strategy via bionanocombinatorics: bifunctional peptides for linking Au and Ag nanomaterials

Materials-binding peptides provide the basis for new nanoparticle assembly strategies.

Influence of polyvinylpyrrolidone (PVP) capping layer on silver nanowire networks: theoretical and experimental studies

By adjusting the polyvinylpyrrolidone (PVP) capping layer thickness on silver nanowire networks, improved electrical and optical properties were obtained, which was confirmed both experimentally and theoretically (Molecular dynamics and Monte Carlo simulations).

Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices

First-principles calculations on nanoscale-sized noble metal nanoparticles demonstrate that planes, edges and vertices show different noncovalent adsorption propensities depending on the adsorbate functional group.

Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation

Computational techniques have the potential to accelerate the design and optimization of nanomaterials for applications such as drug delivery and contaminant removal; however, the success of such techniques requires reliable models of nanomaterial surfaces as well as accurate descriptions of their interactions with relevant solutes. In the present work, we evaluate the ability of selected models of naked and hydroxylated carbon nanotubes to predict adsorption equilibrium constants for about 30 small aromatic compounds with a variety of functional groups. The equilibrium constants determined using molecular dynamics coupled with free-energy calculation techniques are directly compared to those derived from experimental measurements. The calculations are highly predictive of the relative adsorption affinities of the compounds, with excellent correlation (r ≥ 0.9) between calculated and measured values of the logarithm of the adsorption equilibrium constant. Moreover, the agreement in absolute terms is also reasonable, with average errors of less than one decade. We also explore possible effects of surface loading, although we demonstrate that they are negligible for the experimental conditions considered. Given the degree of reliability demonstrated, we move on to employing the in silico techniques in the design of nanomaterials, using the optimization of adsorption affinity for the herbacide atrazine as an example. Our simulations suggest that, compared to other modifications of graphenic carbon, polyvinylpyrrolidone conjugation gives the highest affinity for atrazine-substantially greater than that of graphenic carbon alone-and may be useful as a nanomaterial for delivery or sequestration of atrazine.

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.

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

Molecular dynamics simulations of the aqueous biomolecule–graphene interface have predicted the free energy of adsorption of amino acids and the structure of peptides.

Thermostability and reversibility of silver nanoparticle-protein binding

The interactions between nanoparticles (NPs) and proteins in living systems are a precursor to the formation of a NP-protein "corona" that underlies cellular and organism responses to nanomaterials. However, the thermodynamic properties and reversibility of NP-protein interactions have rarely been examined. Using an automated, high-throughput and temperature-controlled dynamic light scattering (DLS) technique we observed a distinct hysteresis in the hydrodynamic radius of branched polyethyleneimine (BPEI) coated-silver nanoparticles (bAgNPs) exposed to like-charged lysozyme during the processes of heating and cooling, in contrast to the irreversible interactions between bAgNPs and oppositely charged alpha lactalbumin (ALact). Our discrete molecular dynamics (DMD) simulations offered a new molecular insight into the differential structure, dynamics and thermodynamics of bAgNPs binding with the two protein homologs and further revealed the different roles of the capping agents of citrate and BPEI in NP-protein interactions. This study facilitates our understanding of the transformation of nanomaterials in living systems, whose implications range from the field study of nanotoxicology to nanomaterials synthesis, nanobiotechnology and nanomedicine.

Structure of arginine overlayers at the aqueous gold interface: implications for nanoparticle assembly

Adsorption of small biomolecules onto the surface of nanoparticles offers a novel route to generation of nanoparticle assemblies with predictable architectures. Previously, ligand-exchange experiments on citrate-capped gold nanoparticles with the amino acid arginine were reported to support linear nanoparticle assemblies. Here, we use a combination of atomistic modeling with experimental characterization to explore aspects of the assembly hypothesis for these systems. Using molecular simulation, we probe the structural and energetic characteristics of arginine overlayers on the Au(111) surface under aqueous conditions at both low- and high-coverage regimes. In the low-density regime, the arginines lie flat on the surface. At constant composition, these overlayers are found to be lower in energy than the densely packed films, although the latter case appears kinetically stable when arginine is adsorbed via the zwitterion group, exposing the charged guanidinium group to the solvent. Our findings suggest that zwitterion-zwitterion hydrogen bonding at the gold surface and minimization of the electrostatic repulsion between adjacent guanidinium groups play key roles in determining arginine overlayer stability at the aqueous gold interface. Ligand-exchange experiments of citrate-capped gold nanoparticles with arginine derivatives agmatine and N-methyl-l-arginine reveal that modification at the guanidinium group significantly diminishes the propensity for linear assembly of the nanoparticles.