Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations

Adsorption on nanoparticles with surface defects: mean field and energy level approaches

In this work two theoretical approximations, the so-called theoretical approach of energy levels and an extension of the modified mean field approach (TAEL and MMFA, respectively) are applied to the study of surface decoration of modified nanostructures like crystalline nanoparticles. The surface of the nanoparticles is modified by the irreversible random deposition of defects consisting in isolated atoms. Such deposition is carried out until a certain surface density is reached, leaving the rest of the sites available for a second species to adsorb. Through the formulation of the integral equation, the theoretical approaches permit obtaining the adsorption isotherms and the compressibility of the adlayer. The main difference between the two approaches is the degree of details considered in their mathematical formulations: TAEL takes in account all the energy levels meanwhile MMFA only an average. The degree of precision and usefulness of both theories were evaluated in comparison with Monte Carlo simulations in the grand canonical assembly. Several cases were studied: attractive and repulsive lateral interactions and different fraction of defects. The effects of the nanoscale were considered for different types and sizes of nanoparticles. By calculating an integral error, we are able to affirm that TAEL reproduces all the properties of the analyzed quantities from the reference simulated curves. On the other hand, the MMFA performance is good only for a certain limited range of the parameters, however the strength is in the mathematical simplicity compared to TAEL.

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.

Heat Transfer in Gold Interfaces Capped with Thiolated Polyethylene Glycol: A Molecular Dynamics Study

Reverse nonequilibrium molecular dynamics simulations were used to study heat transport in solvated gold interfaces which have been functionalized with a low-molecular weight thiolated polyethylene glycol (PEG). The gold interfaces studied included (111), (110), and (100) facets as well as spherical nanoparticles with radii of 10 and 20 Å. The embedded atom model (EAM) and the polarizable density-readjusted embedded atom model (DR-EAM) were implemented to determine the effect of metal polarizability on heat transport properties. We find that the interfacial thermal conductance values for thiolated PEG-capped interfaces are higher than those for pristine gold interfaces. Hydrogen bonding between the thiolated PEG and solvent differs between planar facets and the nanospheres, suggesting one mechanism for enhanced transfer of energy, while the covalent gold sulfur bond appears to create the largest barrier to thermal conduction. Through analysis of vibrational power spectra, we find an enhanced population at low-frequency heat-carrying modes for the nanospheres, which may also explain the higher mean interfacial thermal conductance (G) value.

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.

Transformation of L-DOPA and Dopamine on the Surface of Gold Nanoparticles: An NMR and Computational Study

Gold nanoparticles (AuNPs) have found applications in biomedicine as diagnostic tools, but extensive research efforts have been also directed toward their development as more efficient drug delivery agents. The high specific surface area of AuNPs may provide dense loading of molecules like catechols (L-DOPA and dopamine) on nanosurfaces, enabling functionalization strategies for advancing conventional therapy and diagnostic approaches of neurodegenerative diseases. Despite numerous well-described procedures in the literature for preparation of different AuNPs, possible transformation and structural changes of surface functionalization agents have not been considered thoroughly. As a case in point, the catechols L-DOPA and dopamine were selected because of their susceptibility to oxidation, cyclization, and polymerization. To assess the fate of coating and functionalization agents during the preparation of AuNPs or interaction at the nano-bio interface, a combination of spectroscopy, light scattering, and microscopy techniques was used while structural information and reaction mechanism were obtained by NMR in combination with computational tools. The results revealed that the final form of catechol on the AuNP nanosurface depends on the molar ratio of Au used for AuNP preparation. A large molar excess of L-DOPA or dopamine is needed to prepare AuNPs funtionalized with fully reduced catechols. In the case of molar excess of Au, the oxidation of catechols to dopamine quinone and dopaquinone was promoted, and dopaquinone underwent intramolecular cyclization in which additional oxidation products, leukodopachrome, dopachrome, or its tautomer, were formed because of the larger intrinsic acidity of the more nucleophilic amino group in dopaquinone. MD simulations showed that, of the oxidation products, dopachrome had the highest affinity for binding to the AuNPs surface. The results highlight how a more versatile methodological approach, combining experimental and in silico techniques, allows more reliable characterization of binding events at the surface of AuNPs for possible applications in biomedicine.

Detection of gold cysteine thiolate complexes on gold nanoparticles with time-of-flight secondary ion mass spectrometry

Gold (Au) nanoparticles (NPs) are widely used in nanomedical applications as a carrier for molecules designed for different functionalities. Previous findings suggested that biological molecules, including amino acids, could contribute to the dissolution of Au NPs in physiological environments and that this phenomenon was size-dependent. We, therefore, investigated the interactions of L-cysteine with 5-nm Au NPs by means of time-of-flight secondary ion mass spectrometry (ToF-SIMS). This was achieved by loading Au NPs on a clean aluminum (Al) foil and immersing it in an aqueous solution containing L-cysteine. Upon rinsing off the excessive cysteine molecules, ToF-SIMS confirmed the formation of gold cysteine thiolate via the detection of not only the Au-S bond but also the hydrogenated gold cysteine thiolate molecular ion. The presence of NaCl or a 2-(N-morpholino)ethanesulfonic acid buffer disabled the detection of Au NPs on the Al foil. The detection of larger (50-nm) Au NPs was possible but resulted in weaker cysteine and gold signals, and no detected gold cysteine thiolate signals. Nano-gold specific adsorption of L-cysteine was also demonstrated by cyclic voltammetry using paraffine-impregnated graphite electrodes with deposited Au NPs. We demonstrate that the superior chemical selectivity and surface sensitivity of ToF-SIMS, via detection of elemental and molecular species, provide a unique ability to identify the adsorption of cysteine and formation of gold-cysteine bonds on Au NPs.

Combined NMR and Computational Study of Cysteine Oxidation during Nucleation of Metallic Clusters in Biological Systems

The widespread biomedical applications of silver and gold nanoparticles (AgNPs and AuNPs, respectively) prompt the need for mechanistic evaluation of their interaction with biomolecules. In biological media, metallic NPs are known to transform by various pathways, especially in the presence of thiols. The interplay between metallic NPs and thiols may lead to unpredictable consequences for the health status of an organism. This study explored the potential events occurring during biotransformation, dissolution, and reformation of NPs in the thiol-rich biological media. The study employed a model system evaluating the interaction of cysteine with small-sized AgNPs and AuNPs. The interplay of cysteine on transformation and reformation pathways of these NPs was experimentally investigated by nuclear magnetic resonance (NMR) spectroscopy and supported by light scattering techniques and transmission electron microscopy (TEM). As the main outcome, Ag- or Au-catalyzed oxidation of cysteine to cystine was found to occur through generation of reactive oxygen species (ROS). Computational simulations confirmed this mechanism and the role of ROS in the oxidative dimerization of biothiol during NPs reformation. The obtained results represent valuable mechanistic data about the complex events during the transport of metallic NPs in thiol-rich biological systems that should be considered for the future biomedical applications of metal-based nanomaterials.

Interface and Interphase in Polymer Nanocomposites with Bare and Core-Shell Gold Nanoparticles

Metal nanoparticles are used to modify/enhance the properties of a polymer matrix for a broad range of applications in bio-nanotechnology. Here, we study the properties of polymer/gold nanoparticle (NP) nanocomposites through atomistic molecular dynamics, MD, simulations. We probe the structural, conformational and dynamical properties of polymer chains at the vicinity of a gold (Au) NP and a functionalized (core/shell) Au NP, and compare them against the behavior of bulk polyethylene (PE). The bare Au NPs were constructed via a systematic methodology starting from ab-initio calculations and an atomistic Wulff construction algorithm resulting in the crystal shape with the minimum surface energy. For the functionalized NPs the interactions between gold atoms and chemically adsorbed functional groups change their shape. As a model polymer matrix we consider polyethylene of different molecular lengths, from the oligomer to unentangled Rouse like systems. The PE/Au interaction is parametrized via DFT calculations. By computing the different properties the concept of the interface, and the interphase as well, in polymer nanocomposites with metal NPs are critically examined. Results concerning polymer density profiles, bond order parameter, segmental and terminal dynamics show clearly that the size of the interface/interphase, depends on the actual property under study. In addition, the anchored polymeric chains change the behavior/properties, and especially the chain density profile and the dynamics, of the polymer chain at the vicinity of the Au NP.

Ion-Specific Adsorption on Bare Gold (Au) Nanoparticles in Aqueous Solutions: Double-Layer Structure and Surface Potentials

We study the solvation and electrostatic properties of bare gold (Au) nanoparticles (NPs) of 1-2 nm in size in aqueous electrolyte solutions of sodium salts of various anions with large physicochemical diversity (Cl^-, BF₄^-, PF₆^-, Nip^- (nitrophenolate), 3- and 4-valent hexacyanoferrate (HCF)) using nonpolarizable, classical molecular dynamics computer simulations. We find a substantial facet selectivity in the adsorption structure and spatial distribution of the ions at the AuNPs: while sodium and some of the anions (e.g., Cl^-, HCF^3-) adsorb more at the "edgy" (100) and (110) facets of the NPs, where the water hydration structure is more disordered, other ions (e.g., BF₄^-, PF₆^-, Nip^-) prefer to adsorb strongly on the extended and rather flat (111) facets. In particular, Nip^-, which features an aromatic ring in its chemical structure, adsorbs strongly and perturbs the first water monolayer structure on the NP (111) facets substantially. Moreover, we calculate adsorptions, radially resolved electrostatic potentials as well as the far-field effective electrostatic surface charges and potentials by mapping the long-range decay of the calculated electrostatic potential distribution onto the standard Debye-Hückel form. We show how the extrapolation of these values to other ionic strengths can be performed by an analytical Adsorption-Grahame relation between the effective surface charge and potential. We find for all salts negative effective surface potentials in the range from -10 mV for NaCl down to about -80 mV for NaNip, consistent with typical experimental ranges for the zeta potential. We discuss how these values depend on the surface definition and compare them to the explicitly calculated electrostatic potentials near the NP surface, which are highly oscillatory in the ±0.5 V range.

Targeting and Inhibiting Plasmodium falciparum Using Ultra-small Gold Nanoparticles

Malaria, a mosquito-borne disease caused by Plasmodium species, claims more than 400,000 lives globally each year. The increasing drug resistance of the parasite renders the development of new anti-malaria drugs necessary. Alternatively, better delivery systems for already marketed drugs could help to solve the resistance problem. Herein, we report glucose-based ultra-small gold nanoparticles (Glc-NCs) that bind to cysteine-rich domains of Plasmodium falciparum surface proteins. Microscopy shows that Glc-NCs bind specifically to extracellular and all intra-erythrocytic stages of P. falciparum. Glc-NCs may be used as drug delivery agents as illustrated for ciprofloxacin, a poorly soluble antibiotic with low antimalarial activity. Ciprofloxacin conjugated to Glc-NCs is more water-soluble than the free drug and is more potent. Glyco-gold nanoparticles that target cysteine-rich domains on parasites may be helpful for the prevention and treatment of malaria.

Rational Design of Functional Peptide-Gold Hybrid Nanomaterials for Molecular Interactions

Gold nanoparticles (AuNPs) have been extensively used for decades in biosensing-related development due to outstanding optical properties. Peptides, as newly realized functional biomolecules, are promising candidates of replacing antibodies, receptors, and substrates for specific molecular interactions. Both peptides and AuNPs are robust and easily synthesized at relatively low cost. Hence, peptide-AuNP-based bio-nano-technological approaches have drawn increasing interest, especially in the field of molecular targeting, cell imaging, drug delivery, and therapy. Many excellent works in these areas have been reported: demonstrating novel ideas, exploring new targets, and facilitating advanced diagnostic and therapeutic technologies. Importantly, some of them also have been employed to address real practical problems, especially in remote and less privileged areas. This contribution focuses on the application of peptide-gold hybrid nanomaterials for various molecular interactions, especially in biosensing/diagnostics and cell targeting/imaging, as well as for the development of highly active antimicrobial/antifouling coating strategies. Rationally designed peptide-gold nanomaterials with functional properties are discussed along with future challenges and opportunities.

Structural surface and thermodynamics analysis of nanoparticles with defects

In this work, we analyze the surface structure and thermodynamics regarding the decoration of nanoparticles with defects, using statistical calculations and Monte Carlo simulations in a complementary way.

One-pot synthesis of 3D Au nanoparticle clusters with tunable size and their application

In general, the preparation of Au nanoparticle clusters (NPCs) is more challenging than that of nanoparticles. The traditional multi-step method for preparing Au NPCs is time consuming and highly sensitive to the reaction conditions. Here, we report a simple and feasible method for the rapid preparation of Au NPCs (∼30 min), in which Au (III) is reduced to Au (0) by trisodium citrate, and assembled into NPCs in the presence of a trace amount of cysteine. The surface plasmon resonance peak of the Au NPCs is tunable and ranged from visible to near-IR regions by varying the content of cysteine added. The growth process of Au NPCs was monitored by dynamic light scattering, UV-vis absorption spectroscopy and transmission electron microscopy. Their elemental composition, chemical state and molecular structure of the sample surface were measured by x-ray photoelectron spectroscopy. The proposed synthesis mechanism has guiding significance for the preparation of other NPCs. Au NPCs used as surface-enhanced Raman spectroscopy substrate has a good enhancement effect because of its unique morphology.

ReaxFF MD Simulations of Peptide-Grafted Gold Nanoparticles

Functionalized gold nanoparticles have critical applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field molecular dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and glycine in different grafting densities in the aqueous environment. Our study showed slight facet-dependent peptide adsorption on a gold nanoparticle with the 3 nm core diameter. Peptide chains prefer to adsorb on the Au(111) facet compared to those on other facets of Au(100) and Au(110). In addition to the stable thiol interaction with gold nanoparticle surfaces, polarizable oxygen and nitrogen atoms show strong interactions with the gold surface and polarize the gold nanoparticle surfaces with an overall positive charge. Charges of gold atoms vary according to their contacts with peptide atoms and lattice positions. However, at the outmost peptide layer, the whole functionalized Au nanoparticles exhibit overall negative electrostatic potential due to the grafted peptides. Moreover, simulations show that thiol groups can be deprotonated and subsequently protons can be transferred to water molecules and carboxyl groups.

Solution NMR Spectroscopy with Isotope-Labeled Cysteine (13C and 15N) Reveals the Surface Structure of l-Cysteine-Coated Ultrasmall Gold Nanoparticles (1.8 nm)

Ultrasmall gold nanoparticles with a diameter of 1.8 nm were synthesized by reduction of tetrachloroauric acid with sodium borohydride in the presence of l-cysteine, with natural isotope abundance as well as ¹³C-labeled and ¹⁵N-labeled. The particle diameter was determined by high-resolution transmission electron microscopy and differential centrifugal sedimentation. X-ray photoelectron spectroscopy confirmed the presence of metallic gold with only a few percent of oxidized Au(+I) species. The surface structure and the coordination environment of the cysteine ligands on the ultrasmall gold nanoparticles were studied by a variety of homo- and heteronuclear NMR spectroscopic techniques including ¹H-¹³C-heteronuclear single-quantum coherence and ¹³C-¹³C-INADEQUATE. Further information on the binding situation (including the absence of residual or detached l-cysteine in the solution) and on the nanoparticle diameter (indicating the well-dispersed state) was obtained by diffusion-ordered spectroscopy (¹H-, ¹³C-, and ¹H-¹³C-DOSY). Three coordination environments of l-cysteine on the gold surface were identified that were ascribed to different crystallographic sites, supported by geometric considerations of the nanoparticle ultrastructure. The particle size data and the NMR-spectroscopic analysis gave a particle composition of about Au₁₇₄(cysteine)₆₇.

Structure and dynamics of gold nanoparticles decorated with chitosan–gentamicin conjugates: ReaxFF molecular dynamics simulations to disclose drug delivery

Functionalized gold nanoparticles for antibiotic drug delivery: from the nanoscale to the atomic scale.

Probing nano-patterned peptide self-organisation at the aqueous graphene interface

The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge-charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions.

Characterization of the adsorption dynamics of trisodium citrate on gold in water solution

Functionalization of a gold nanoparticle with citric acid.