Studies of Dynamic Binding of Amino Acids to TiO2 Nanoparticle Surfaces by Solution NMR and Molecular Dynamics Simulations

Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning

Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.

Modulating the toxicity of engineered nanoparticles by controlling protein corona formation: Recent advances and future prospects

With the rapid development and widespread application of engineered nanoparticles (ENPs), understanding the fundamental interactions between ENPs and biological systems is essential to assess and predict the fate of ENPs in vivo. When ENPs are exposed to complex physiological environments, biomolecules quickly and inevitably adsorb to ENPs to form a biomolecule corona, such as a protein corona (PC). The formed PC has a significant effect on the physicochemical properties of ENPs and gives them a brand new identity in the biological environment, which determines the subsequent ENP-cell/tissue/organ interactions. Controlling the formation of PCs is therefore of utmost importance to accurately predict and optimize the behavior of ENPs within living organisms, as well as ensure the safety of their applications. In this review, we provide an overview of the fundamental aspects of the PC, including the formation mechanism, composition, and frequently used characterization techniques. We comprehensively discuss the potential impact of the PC on ENP toxicity, including cytotoxicity, immune response, and so on. Additionally, we summarize recent advancements in manipulating PC formation on ENPs to achieve the desired biological outcomes. We further discuss the challenges and prospects, aiming to provide valuable insights for a better understanding and prediction of ENP behaviors in vivo, as well as the development of low-toxicity ENPs.

Gaussian attractive potential for carboxylate/cobalt surface interactions

Ligand-decorated metal surfaces play a pivotal role in various areas of chemistry, particularly in selective catalysis. Molecular dynamics simulations at the molecular mechanics level of theory are best adapted to gain complementary insights to experiments regarding the structure and dynamics of such organic films. However, standard force fields tend to capture only weak physisorption interactions. This is inadequate for ligands that are strongly adsorbed such as carboxylates on metal surfaces. To address this limitation, we employ the Gaussian Lennard-Jones (GLJ) potential, which incorporates an attractive Gaussian potential between the surface and ligand atoms. Here, we develop this approach for the interaction between cobalt surfaces and carboxylate ligands. The accuracy of the GLJ approach is validated through the analysis of the interaction of oxygen with two distinct cobalt surfaces. The accuracy of this method reaches a root mean square deviation (RMSD) of about 3 kcal/mol across all probed configurations, which corresponds to a percentage error of roughly 4%. Application of the GLJ force field to the dynamics of the organic layer on these surfaces reveals how the ligand concentration influences the film order, and highlights differing mobility in the x and y directions, attributable to surface corrugation on Co(112̄0). GLJ is versatile, suitable for a broad range of metal/ligand systems, and can, subsequently, be utilized to study the organic film on the adsorption/desorption of reactants and products during a catalytic process.

Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating

The understanding of interactions between nanomaterials and biological molecules is of primary importance for biomedical applications of nanomaterials, as well as for the evaluation of their possible toxic effects. Here, we carried out extensive molecular dynamics simulations of the adsorption properties of about 30 small molecules representing biomolecular fragments at ZnS surfaces in aqueous media. We computed adsorption free energies and potentials of mean force of amino acid side chain analogs, lipids, and sugar fragments to ZnS (110) crystal surface and to a spherical ZnS nanoparticle. Furthermore, we investigated the effect of poly-methylmethacrylate (PMMA) coating on the adsorption preferences of biomolecules to ZnS. We found that only a few anionic molecules: aspartic and glutamic acids side chains, as well as the anionic form of cysteine show significant binding to pristine ZnS surface, while other molecules show weak or no binding. Spherical ZnS nanoparticles show stronger binding of these molecules due to binding at the edges between different surface facets. Coating of ZnS by PMMA changes binding preferences drastically: the molecules that adsorb to a pristine ZnS surface do not adsorb on PMMA-coated surfaces, while some others, particularly hydrophobic or aromatic amino-acids, show high binding affinity due to binding to the coating. We investigate further the hydration properties of the ZnS surface and relate them to the binding preferences of biomolecules.

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction

Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.

Binding Between Antibiotics and Polystyrene Nanoparticles Examined by NMR

Elucidating the interactions between plastic nanoparticles and small molecules is important to understanding these interactions as they occur in polluted waterways. For example, plastic that breaks down into micro- and nanoscale particles will interact with small molecule pollutants that are also present in contaminated waters. Other components of natural water, such as dissolved organic matter, will also influence these interactions. Here we use a collection of complementary NMR techniques to examine the binding between polystyrene nanoparticles and three common antibiotics, belonging to a class of molecules that are expected to be common in polluted water. Through examination of proton NMR signal intensity, relaxation times, saturation-transfer difference (STD) NMR, and competition STD-NMR, we find that the antibiotics have binding strengths in the order amoxicillin < metronidazole ≪ levofloxacin. Levofloxacin is able to compete for binding sites, preventing the other two antibiotics from binding. The presence of tannic acid disrupts the binding between levofloxacin and the polystyrene nanoparticles, but does not influence the binding between metronidazole and these nanoparticles.

Solution NMR methods for structural and thermodynamic investigation of nanoparticle adsorption equilibria

Characterization of dynamic processes occurring at the nanoparticle (NP) surface is crucial for developing new and more efficient NP catalysts and materials. Thus, a vast amount of research has been dedicated to developing techniques to characterize sorption equilibria. Over recent years, solution NMR spectroscopy has emerged as a preferred tool for investigating ligand-NP interactions. Indeed, due to its ability to probe exchange dynamics over a wide range of timescales with atomic resolution, solution NMR can provide structural, kinetic, and thermodynamic information on sorption equilibria involving multiple adsorbed species and intermediate states. In this contribution, we review solution NMR methods for characterizing ligand-NP interactions, and provide examples of practical applications using these methods as standalone techniques. In addition, we illustrate how the integrated analysis of several NMR datasets was employed to elucidate the role played by support-substrate interactions in mediating the phenol hydrogenation reaction catalyzed by ceria-supported Pd nanoparticles.

Aggregation Properties of Albumin in Interacting with Magnetic Fluids

In this study, interactions of Fe3O4 magnetic nanoparticles with serum albumin biomolecules in aqueous solutions were considered. The studies were conducted with the laser correlation spectroscopy and optical analysis of dehydrated films. It was shown that the addition of magnetite to an albumin solution at low concentrations of up to 10-6 g/L led to the formation of aggregates with sizes of up to 300 nm in the liquid phase and an increase in the number of spiral structures in the dehydrated films, which indicated an increase in their stability. With a further increase in the magnetite concentration in the solution (from 10-4 g/L), the magnetic particles stuck together and to albumin, thus forming aggregates with sizes larger than 1000 nm. At the same time, the formation of morphological structures in molecular films was disturbed, and a characteristic decrease in their stability occurred. Most stable films were formed at low concentrations of magnetic nanoparticles (less than 10-4 g/L) when small albumin-magnetic nanoparticle aggregates were formed. These results are important for characterizing the interaction processes of biomolecules with magnetic nanoparticles and can be useful for predicting the stability of biomolecular films with the inclusion of magnetite particles.

Environmental Aspects of Oxide Nanoparticles: Probing Oxide Nanoparticle Surface Processes Under Different Environmental Conditions

Surface chemistry affects the physiochemical properties of nanoparticles in a variety of ways. Therefore, there is great interest in understanding how nanoparticle surfaces evolve under different environmental conditions of pH and temperature. Here, we discuss the use of vibrational spectroscopy as a tool that allows for in situ observations of oxide nanoparticle surfaces and their evolution due to different surface processes. We highlight oxide nanoparticle surface chemistry, either engineered anthropogenic or naturally occurring geochemical nanoparticles, in complex media, with a focus on the impact of (a) pH on adsorption, intermolecular interactions, and conformational changes; (b) surface coatings and coadsorbates on protein adsorption kinetics and protein conformation; (c) surface adsorption on the temperature dependence of protein structure phase changes; and (d) the use of two-dimensional correlation spectroscopy to analyze spectroscopic results for complex systems. An outlook of the field and remaining challenges is also presented.

Binding Mode Characterization of Osteopontin on Hydroxyapatite by Solution NMR Spectroscopy

Extracellular matrix glycoproteins play a major role in bone mineralization and modulation of osteogenesis. Among these, the intrinsically disordered protein osteopontin (OPN) is associated with the inhibition of formation, growth and proliferation of the bone mineral hydroxyapatite (HAP). Furthermore, post-translational modifications like phosphorylation can alter conformations and interaction properties of intrinsically disordered proteins (IDPs). Therefore, the actual interaction of OPN with a HAP surface on an atomic level and how this interaction is affected by phosphorylation is of great interest. Here, we study the interaction of full-length OPN on the surface of suspended HAP nanoparticles by solution NMR spectroscopy. We report the binding modes of this IDP and provide evidence for the influence of hyperphosphorylation on the binding character and an explanation for the differing roles in biomineralization. Our study moreover presents an easy and suitable option to measure interaction of nanoparticles in a stable suspension with full-length proteins.

Molecular dynamics simulations of amino acid adsorption and transport at the acetonitrile–water–silica interface: the role of side chains

The solvation and transport of amino acid residues at liquid–solid interfaces have great importance for understanding the mechanism of separation of biomolecules in liquid chromatography. This study uses umbrella sampling molecular dynamics simulations to study the adsorption and transport of three amino acid molecules with different side chains (phenylalanine (Phe), leucine (Leu) and glutamine (Gln)) at the silica–water–acetonitrile interface in liquid chromatography. Free energy analysis shows that the Gln molecule has stronger binding affinity than the other two molecules, indicating the side chain polarity may play a primary role in adsorption at the liquid–solid interface. The Phe molecule with a phenyl side chain exhibits stronger adsorption free energy than Leu with a non-polar side chain, which can be ascribed to the better solvated configuration of Phe. Further analysis of molecular orientations found that the amino acid molecules with apolar side chains (Phe and Leu) have ‘standing up’ configurations at their stable adsorption state, where the polar functional groups are close to the interface and the side chain is far from the interface, whereas the amino acid molecule with a polar side chain (Gln) chooses the ‘lying’ configuration, and undergoes a sharp orientation transition when the molecule moves away from the silica surface. Extending our simulation studies to systems with different solute concentrations reveals that there is a decrease in the adsorption free energy as well as surface diffusion as the solute concentration increases, which is related to the crowding in the interfacial layers. This simulation study gives a detailed microscopic description of amino acid molecule solvation and transport at the acetonitrile–water–silica interface in liquid chromatography and will be helpful for understanding the retention mechanism for amino acid separation.

The solvation and transport of amino acid residues at liquid–solid interfaces have great importance for understanding the mechanism of separation of biomolecules in liquid chromatography.

An organogel library for solution NMR analysis of nanoparticle suspensions in non-aqueous samples

Surface contrast solution NMR methods (scNMR) are emerging as powerful tools to investigate the adsorption of small molecule ligands to the surface of nanoparticles (NP), returning fundamental insight into the kinetics and thermodynamics of sorption, as well as structural information on the adsorbed species. A prerequisite for the acquisition of high quality solution NMR data is the preparation of homogeneous and stable samples that return consistent NMR spectra and allow extensive signal averaging. Unfortunately, this condition does not apply to NMR samples containing NPs that often show a tendency to sediment and accumulate at the bottom of the NMR tube over the course of the experiment. We have recently shown that preparing NMR samples in an agarose gel matrix inhibits sedimentation and allows the characterization of small molecule-NP interactions by scNMR. Unfortunately, as the agarose gel only forms in aqueous solution, this sample preparation method cannot be used to stabilize NP suspensions in a non-aqueous environment. Here, we introduce a library of 48 organogels, based on low molecular-mass organic gelators (LMOGs), to prepare NMR samples of small molecule/NP systems in a wide range of organic solvents. In addition, we present a simple method that takes advantage of ¹H transverse relaxation (¹H-R₂) measurements to screen the library and identify the best gelator to characterize the small molecule-NP interaction of interest in the solvent of choice. We expect the results of this study will enable the preparation of homogeneous and stable samples of NPs in non-aqueous environments, therefore dramatically increasing the applicability of scNMR to the characterization of heterogeneous interactions and to the investigation of the role played by solvent molecules in regulating the kinetics and thermodynamics of sorption.