Quantitative analysis of scanning tunneling microscopy images of mixed-ligand-functionalized nanoparticles

Synthetic Data in Quantitative Scanning Probe Microscopy

Synthetic data are of increasing importance in nanometrology. They can be used for development of data processing methods, analysis of uncertainties and estimation of various measurement artefacts. In this paper we review methods used for their generation and the applications of synthetic data in scanning probe microscopy, focusing on their principles, performance, and applicability. We illustrate the benefits of using synthetic data on different tasks related to development of better scanning approaches and related to estimation of reliability of data processing methods. We demonstrate how the synthetic data can be used to analyse systematic errors that are common to scanning probe microscopy methods, either related to the measurement principle or to the typical data processing paths.

Cancer Nanopharmaceuticals: Physicochemical Characterization and In Vitro/In Vivo Applications

Physicochemical, pharmacokinetic, and biopharmaceutical characterization tools play a key role in the assessment of nanopharmaceuticals' potential imaging analysis and for site-specific delivery of anti-cancers to neoplastic cells/tissues. If diagnostic tools and therapeutic approaches are combined in one single nanoparticle, a new platform called nanotheragnostics is generated. Several analytical technologies allow us to characterize nanopharmaceuticals and nanoparticles and their properties so that they can be properly used in cancer therapy. This paper describes the role of multifunctional nanoparticles in cancer diagnosis and treatment, describing how nanotheragnostics can be useful in modern chemotherapy, and finally, the challenges associated with the commercialization of nanoparticles for cancer therapy.

Nanostructured surfaces from ligand-protected metal nanoparticles

Nanostructuring surfaces with metal atoms or clusters represents a promising approach to create materials with unique electronic/magnetic properties and improved chemical reactivity. By means of plasma sputtering and mass spectrometric techniques, the deposition of precisely size-selected clusters onto single-crystal surfaces has been applied to prepare surfaces with tailored properties. However, nanostructured surfaces can as well be prepared with metal nanoparticles via solution-phase methods, but the difference is that nanoparticles prepared by wet chemistry are usually coated with a layer of ligands, which are essential not only for maintaining the size and the atomic structure of metallic cores, but also for playing crucial roles in the synthesis, physicochemical properties and catalytic activities of the nanoparticles. This Frontier covers aspects of nanostructured surfaces from ligand-protected metal nanoparticles, starting with high-resolution imaging of the ligand-protected metal nanoparticles, followed by periodic patterning of metal nanoparticles on surfaces and the well-controlled atomic layer deposition with nanoclusters at the liquid/solid interface. We also highlight the potential of the surface-supported structures from ligand-protected metal nanoparticles, and the challenges remaining to be tackled.

Structure Evolution of Binary Ligands on Nanoparticles Triggered by Competition between Adsorption Reaction and Phase Separation

The ligand shell of a nanoparticle (NP) determines most of the interfacial properties through its composition and structure. Despite widespread study over the years, the factors impacting the ligand shell structures, especially the effects of ligand-adsorption kinetics in solution, are still not clear and even conflict with each other. We have developed an adsorption-migration reaction model to study the dynamic evolution processes of binary ligands on NP surfaces during adsorption reaction. Apparent dependence of the structure of ligand shells on ligand-adsorption and phase-separation rates has been found, which induces the formation of different shell patterns, including Janus, patchy, stripe, and island patterns. The formation process of these patterns accords with different reaction kinetic pathways, depending on the nature of ligands. Further screening the role of the NPs' curvature reveals that it can indirectly influence the ligand-adsorption and phase-separation kinetics. As the NPs' curvature increases, an accelerated ligand-adsorption and phase-separation process on NPs will happen, resulting in the preferential formation of more ordered Janus or stripe patterns. These results suggest that controlling the reaction kinetics is key to effectively regulating the composition and morphology of binary ligands on NPs. They also provide principles for guiding the experimental studies to fabricate novel NPs with a functional surface for use in broad nanoscience fields.

Mixed Fluorinated/Hydrogenated Self-Assembled Monolayer-Protected Gold Nanoparticles: In Silico and In Vitro Behavior

Gold nanoparticles (AuNPs) covered with mixtures of immiscible ligands present potentially anisotropic surfaces that can modulate their interactions at complex nano-bio interfaces. Mixed, self-assembled, monolayer (SAM)-protected AuNPs, prepared with incompatible hydrocarbon and fluorocarbon amphiphilic ligands, are used here to probe the molecular basis of surface phase separation and disclose the role of fluorinated ligands on the interaction with lipid model membranes and cells, by integrating in silico and experimental approaches. These results indicate that the presence of fluorinated amphiphilic ligands enhances the membrane binding ability and cellular uptake of gold nanoparticles with respect to those coated only with hydrogenated amphiphilic ligands. For mixed monolayers, computational results suggest that ligand phase separation occurs on the gold surface, and the resulting anisotropy affects the number of contacts and adhesion energies with a membrane bilayer. This reflects in a diverse membrane interaction for NPs with different surface morphologies, as determined by surface plasmon resonance, as well as differential effects on cells, as observed by flow cytometry and confocal microscopy. Overall, limited changes in monolayer features can significantly affect NP surface interfacial properties, which, in turn, affect the interaction of SAM-AuNPs with cellular membranes and subsequent effects on cells.

Mass spectrometry and Monte Carlo method mapping of nanoparticle ligand shell morphology

Janus, patchy, stripe-like, or random arrangements of molecules within the ligand shell of nanoparticles affect many properties. Among all existing ligand shell morphology characterization methods, the one based on mass spectroscopy is arguably the simplest. Its greatest limitation is that the results are qualitative. Here, we use a tailor-made Monte Carlo type program that fits the whole MALDI spectrum and generates a 3D model of the ligand shell. Quantitative description of the ligand shell in terms of nearest neighbor distribution and characteristic length scale can be readily extracted by the model, and are compared with the results of other characterization methods. A parameter related to the intermolecular interaction is extracted when this method is combined with NMR. This approach could become the routine method to characterize the ligand shell morphology of many nanoparticles and we provide an open access program to facilitate its use.

Determining the arrangement of ligands on a nanoparticle is challenging, given the limitations of existing characterization tools. Here, the authors describe an accessible method for resolving ligand shell morphology that uses simple MALDI-TOF mass spectrometry measurements in conjunction with an open-access Monte Carlo fitting program.

Real-space imaging with pattern recognition of a ligand-protected Ag374 nanocluster at sub-molecular resolution

High-resolution real-space imaging of nanoparticle surfaces is desirable for better understanding of surface composition and morphology, molecular interactions at the surface, and nanoparticle chemical functionality in its environment. However, achieving molecular or sub-molecular resolution has proven to be very challenging, due to highly curved nanoparticle surfaces and often insufficient knowledge of the monolayer composition. Here, we demonstrate sub-molecular resolution in scanning tunneling microscopy imaging of thiol monolayer of a 5 nm nanoparticle Ag₃₇₄ protected by tert-butyl benzene thiol. The experimental data is confirmed by comparisons through a pattern recognition algorithm to simulated topography images from density functional theory using the known total structure of the Ag₃₇₄ nanocluster. Our work demonstrates a working methodology for investigations of structure and composition of organic monolayers on curved nanoparticle surfaces, which helps designing functionalities for nanoparticle-based applications.

Translating high-resolution imaging methods to the curved organic surface of a nanoparticle has been challenging. Here, the authors are able to spatially resolve the sub-molecular surface details of a silver nanocluster by comparing scanning tunneling microscopy images and simulated topography data through a pattern recognition algorithm.

Self-assembled monolayers in organic electronics

Self-assembly is possibly the most effective and versatile strategy for surface functionalization. Self-assembled monolayers (SAMs) can be formed on (semi-)conductor and dielectric surfaces, and have been used in a variety of technological applications. This work aims to review the strategy behind the design and use of self-assembled monolayers in organic electronics, discuss the mechanism of interaction of SAMs in a microscopic device, and highlight the applications emerging from the integration of SAMs in an organic device. The possibility of performing surface chemistry tailoring with SAMs constitutes a versatile approach towards the tuning of the electronic and morphological properties of the interfaces relevant to the response of an organic electronic device. Functionalisation with SAMs is important not only for imparting stability to the device or enhancing its performance, as sought at the early stages of development of this field. SAM-functionalised organic devices give rise to completely new types of behavior that open unprecedented applications, such as ultra-sensitive label-free biosensors and SAM/organic transistors that can be used as robust experimental gauges for studying charge tunneling across SAMs.

Gold nanoparticles with patterned surface monolayers for nanomedicine: current perspectives

Molecular self-assembly is a topic attracting intense scientific interest. Various strategies have been developed for construction of molecular aggregates with rationally designed properties, geometries, and dimensions that promise to provide solutions to both theoretical and practical problems in areas such as drug delivery, medical diagnostics, and biosensors, to name but a few. In this respect, gold nanoparticles covered with self-assembled monolayers presenting nanoscale surface patterns-typically patched, striped or Janus-like domains-represent an emerging field. These systems are particularly intriguing for use in bio-nanotechnology applications, as presence of such monolayers with three-dimensional (3D) morphology provides nanoparticles with surface-dependent properties that, in turn, affect their biological behavior. Comprehensive understanding of the physicochemical interactions occurring at the interface between these versatile nanomaterials and biological systems is therefore crucial to fully exploit their potential. This review aims to explore the current state of development of such patterned, self-assembled monolayer-protected gold nanoparticles, through step-by-step analysis of their conceptual design, synthetic procedures, predicted and determined surface characteristics, interactions with and performance in biological environments, and experimental and computational methods currently employed for their investigation.

Characterization of Ligand Shell for Mixed-Ligand Coated Gold Nanoparticles

Gold nanoparticles owe a large number of their properties to their ligand shell. Indeed, many researchers routinely use mixtures of ligand molecules for their nanoparticles to impart complex property sets. It has been shown that the morphology of ligand shells (e.g., Janus, random, stripelike) leads to specific properties. Examples include wettability, solubility, protein nonspecific adsorption, cell penetration, catalysis, and cation-capturing abilities. Yet, it remains a great challenge to evaluate such morphologies in even the most fundamental terms such as dimension and shape. In this Account, we review recent progress in characterization techniques applicable to gold nanoparticles with ligand shells composed of mixed ligands. We divide the characterization into three major categories, namely, microscopy, spectroscopy, and simulation. In microscopy, we review progresses in scanning tunneling microscopy (STM), atomic force microscopy (AFM), and scanning/transmission electron microscopy. In spectroscopy, we mainly highlight recent achievements in nuclear magnetic resonance (NMR), mass spectrometry (MS), small angle neutron scattering (SANS), electron spin resonance (EPR), and adsorption based spectroscopies. In simulation, we point out the latest results in understanding thermodynamic stability of ligand shell morphology and emphasize the role of computer simulation for helping interpretation of experimental data. We conclude with a perspective of future development.

Structure and extreme ultraviolet performance of Si/C multilayers deposited under different working pressures

Narrow bandwidth Si/C multilayer mirrors are fabricated and characterized for the Z-pinch plasma diagnostic at a wavelength of 16.5 nm. To reduce the large stress of the multilayer and maintain a practical reflectivity, different working pressures, from 0.13 Pa to 0.52 Pa, are optimized during the deposition. The grazing incidence x-ray reflectometry (GIXR) measurement and the fitting results indicate that an interlayer was formed at the interfaces, while both the interlayer thickness and interface widths increase with larger working pressure. The surface roughness of the multilayers also increases from 0.13 nm at 0.13 Pa to 0.29 nm at 0.52 Pa, as revealed by the atomic force microscope (AFM) measurements. The multilayer stress decreases from -682 MPa to -384  MPa as the working pressure increases from 0.13 Pa to 0.52 Pa, respectively. The experimental extreme ultraviolet (EUV) reflectivity of the samples with 20 bilayers gradually decreased from 26.3% to 18.9% with increased working pressure. The bandwidth of the reflection peak remains similar for the different samples with a full width half-maximum (FWHM) value of around 0.87 nm. A maximum EUV reflectivity of 33.2% and a bandwidth of 0.64 nm were achieved by the sample with 50 bilayers fabricated under a working pressure of 0.13 Pa.

Response to "Critical Assessment of the Evidence for Striped Nanoparticles"

Stirling et al., (10.1371/journal.pone.0108482) presented an analysis on some of our publications on the formation of stripe-like domains on mixed-ligand coated gold nanoparticles. The authors shed doubts on some of our results however no valid argument is provided against what we have shown since our first publication: scanning tunneling microscopy (STM) images of striped nanoparticles show stripe-like domains that are independent of imaging parameters and in particular of imaging speed. We have consistently ruled out the presence of artifacts by comparing sets of images acquired at different tip speeds, finding invariance of the stipe-like domains. Stirling and co-workers incorrectly analyzed this key control, using a different microscope and imaging conditions that do not compare to ours. We show here data proving that our approach is rigorous. Furthermore, we never solely relied on image analysis to draw our conclusions; we have always used the chemical nature of the particles to assess the veracity of our images. Stirling et al. do not provide any justification for the spacing of the features that we find on nanoparticles: ~1 nm for mixed ligand particles and ~ 0.5 nm for homoligand particles. Hence our two central arguments remain unmodified: independence from imaging parameters and dependence on ligand shell chemical composition. The paper report observations on our STM images; none is a sufficient condition to prove that our images are artifacts. We thoroughly addressed issues related to STM artifacts throughout our microscopy work. Stirling et al. provide guidelines for what they consider good STM images of nanoparticles, such images are indeed present in our literature. They conclude that the evidences we provided to date are insufficient, this is a departure from one of the authors’ previous article which concluded that our images were composed of artifacts. Given that four independent laboratories have reproduced our measurements and that no scientifically rigorous argument is presented to invalidate our STM images, and also given that Stirling et al. do not contest the quality of our recent STM images, we re-affirm that specific binary mixture of ligands spontaneously form features in their ligand shell that we describe as stripe-like domains ~1 nm in width.

Nanoparticle characterization based on STM and STS

Scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) can characterize intriguing nanoparticle properties towards solid-state nanodevices.

Aggregation of Aß(25-35) on DOPC and DOPC/DHA bilayers: an atomic force microscopy study

β amyloid peptide plays an important role in both the manifestation and progression of Alzheimer disease. It has a tendency to aggregate, forming low-molecular weight soluble oligomers, higher-molecular weight protofibrillar oligomers and insoluble fibrils. The relative importance of these single oligomeric-polymeric species, in relation to the morbidity of the disease, is currently being debated. Here we present an Atomic Force Microscopy (AFM) study of Aβ(25–35) aggregation on hydrophobic dioleoylphosphatidylcholine (DOPC) and DOPC/docosahexaenoic 22∶6 acid (DHA) lipid bilayers. Aβ(25–35) is the smallest fragment retaining the biological activity of the full-length peptide, whereas DOPC and DOPC/DHA lipid bilayers were selected as models of cell-membrane environments characterized by different fluidity. Our results provide evidence that in hydrophobic DOPC and DOPC/DHA lipid bilayers, Aβ(25-35) forms layered aggregates composed of mainly annular structures. The mutual interaction between annular structures and lipid surfaces end-results into a membrane solubilization. The presence of DHA as a membrane-fluidizing agent is essential to protect the membrane from damage caused by interactions with peptide aggregates; to reduces the bilayer defects where the delipidation process starts.

Flattening mountains: micro-fabrication of planar replicas for bullet lateral striae analysis

The application of replica molding has proven to be a valuable tool in the analysis of different forensic evidences in particular for its ability to extract the toolmarks from complex sample surfaces. A well known problem in the analysis of ballistic evidences is the accurate characterization of the lateral striae of real bullets seized on crime scenes after shots, due primarily to impact deformations and to unpredictable issues related to laboratory illumination setup. To overcome these problems a possible way is to confine over a flat surface all the features still preserving their three dimensionality. This can be achieved by a novel application of replica molding performed onto the relevant lateral portion of the bullet surface. A quasi-two-dimensional negative copy of the original tridimensional indented surface has been thus fabricated. It combines the real tridimensional topography of class characteristics (land and groove impressions) and of individual caracteristics (striae) impressed by rifled barrels on projectiles, moreover with the possibility of quantitative characterization of these features in a planar configuration, that will allow one-shot comparison of the "whole striae landscape" without the typical artifacts arising from the bullet shape and the illumination issue. A detailed analysis has been carried on at the morphological level by standard optical and scanning electron microscopy, while the 3D topography has been characterized by white light optical profilometry. A quantitative characterization of toolmarks of bullets derived from ammunitions shot by guns of large diffusion, as the Beretta 98 FS cal. 9×21 mm, has been performed and will be presented ranging between the whole landscape and the sub-μm resolution. To investigate the real potentiality of this technique, the experiment has been extended to highly impact-deformed projectiles.

Critical assessment of the evidence for striped nanoparticles

There is now a significant body of literature which reports that stripes form in the ligand shell of suitably functionalised Au nanoparticles. This stripe morphology has been proposed to strongly affect the physicochemical and biochemical properties of the particles. We critique the published evidence for striped nanoparticles in detail, with a particular focus on the interpretation of scanning tunnelling microscopy (STM) data (as this is the only technique which ostensibly provides direct evidence for the presence of stripes). Through a combination of an exhaustive re-analysis of the original data, in addition to new experimental measurements of a simple control sample comprising entirely unfunctionalised particles, we show that all of the STM evidence for striped nanoparticles published to date can instead be explained by a combination of well-known instrumental artefacts, or by issues with data acquisition/analysis protocols. We also critically re-examine the evidence for the presence of ligand stripes which has been claimed to have been found from transmission electron microscopy, nuclear magnetic resonance spectroscopy, small angle neutron scattering experiments, and computer simulations. Although these data can indeed be interpreted in terms of stripe formation, we show that the reported results can alternatively be explained as arising from a combination of instrumental artefacts and inadequate data analysis techniques.

Comparative STM studies of mixed ligand monolayers on gold nanoparticles in air and in 1-phenyloctane

Scanning tunnelling microscopy (STM) studies have found stripe-like domains on gold nanoparticles (NPs) coated with certain binary mixtures of ligand molecules. The majority of these NPs' properties have been investigated for particles in solvents. Yet, most STM studies are for NPs in a dry state. Images of the same particles in air and liquid have not been obtained yet. In this work, a judicious choice of ligand molecules led to NPs with close-to-ideal STM imaging conditions in air and in 1-phenyloctane (PO). Large datasets under both conditions were acquired and rapidly evaluated through power spectral density (PSD) analysis. The result is a quantitative comparison of stripe-like domains in air and PO on the same NPs. PSD analysis determines a characteristic length-scale for these domains of ~1.0 nm in air and in PO showing persistence of striped domains in these two media. A length scale of ~0.7 nm for homoligand NPs was found.

A general mechanism for intracellular toxicity of metal-containing nanoparticles

The assessment of the risks exerted by nanoparticles is a key challenge for academic, industrial, and regulatory communities worldwide. Experimental evidence points towards significant toxicity for a range of nanoparticles both in vitro and in vivo. Worldwide efforts aim at uncovering the underlying mechanisms for this toxicity. Here, we show that the intracellular ion release elicited by the acidic conditions of the lysosomal cellular compartment--where particles are abundantly internalized--is responsible for the cascading events associated with nanoparticles-induced intracellular toxicity. We call this mechanism a "lysosome-enhanced Trojan horse effect" since, in the case of nanoparticles, the protective cellular machinery designed to degrade foreign objects is actually responsible for their toxicity. To test our hypothesis, we compare the toxicity of similar gold particles whose main difference is in the internalization pathways. We show that particles known to pass directly through cell membranes become more toxic when modified so as to be mostly internalized by endocytosis. Furthermore, using experiments with chelating and lysosomotropic agents, we found that the toxicity mechanism for different metal containing NPs (such as metallic, metal oxide, and semiconductor NPs) is mainly associated with the release of the corresponding toxic ions. Finally, we show that particles unable to release toxic ions (such as stably coated NPs, or diamond and silica NPs) are not harmful to intracellular environments.

Control theory for scanning probe microscopy revisited

We derive a theoretical model for studying SPM feedback in the context of control theory. Previous models presented in the literature that apply standard models for proportional-integral-derivative controllers predict a highly unstable feedback environment. This model uses features specific to the SPM implementation of the proportional-integral controller to give realistic feedback behaviour. As such the stability of SPM feedback for a wide range of feedback gains can be understood. Further consideration of mechanical responses of the SPM system gives insight into the causes of exciting mechanical resonances of the scanner during feedback operation.