Two-Dimensional Layered Nanomaterials Steering Self-Assembly of Dodecapeptides with Three Building Blocks.

Self-assembly of peptides on layered nanomaterials such as graphite and MoS2 in the formation of long-range ordered two-dimensional nanocrystal patterns leading to its potential applications for biosensing and bioelectronics has attracted significant interest in nanoscience and nanotechnology. However, controlling the self-assembly of peptides on nanomaterials is still challenging due to the unclear role of nanomaterials in steering self-assembly. Here, we used the in-situ AFM technique to capture different changes of peptide coverage as well as lengthening and widening rates depending on peptide concentrations, show the distinct boundary dynamics of two stabilized peptide domains, and resolve the molecular resolution structural differences and specific orientation of peptide on both nanomaterials. Moreover, ex-situ results showed that the nanomaterial layers tuned the opposite changes of nanowire heights and densities and displayed the different water-resistance stabilities on both nanomaterials. This work provides a basis for understanding nanomaterials steering peptide self-assembly and using hybrid bionanomaterials as a scaffold, enabling for potential biosensing and bioelectronics applications.

Dynamics of Molecular Self-Assembly of Short Peptides at Liquid-Solid Interfaces - Effect of Charged Amino Acid Point Mutations.

Self-organizing solid-binding peptides on atomically flat solid surfaces offer a unique bio/nano hybrid platform, useful for understanding the basic nature of biology/solid coupling and their practical applications. The surface behavior of peptides is determined by their molecular folding, which is influenced by various factors and is challenging to study. Here, the effect of charged amino acids is studied on the self-assembly behavior of a directed evolution selected graphite-binding dodecapeptide on graphite surface. Two mutations, M6 and M8, are designed to introduce negatively and positively charged moieties, respectively, at the anchoring domain of the wild-type (WT) peptide, affecting both binding and assembly. The questions addressed here are whether mutant peptides exhibit molecular crystal formation and demonstrate molecular recognition on the solid surface based on the specific mutations. Frequency-modulated atomic force microscopy is used for observations of the surface processes dynamically in water at molecular resolution over several hours at the ambient. The results indicate that while the mutants display distinct folding and surface behavior, each homogeneously nucleates and forms 2D self-organized patterns, akin to the WT peptide. However, their growth dynamics, domain formation, and crystalline lattice structures differ significantly. The results represent a significant step toward the rational design of bio/solid interfaces, potent facilitators of a variety of future implementations.

Synthesis of optically active star polymers consisting of helical poly(phenylacetylene) chains by the living polymerization of phenylacetylenes and their chiroptical properties.

Star polymers consisting of three helical poly(phenylacetylene) chains with a precisely controlled molecular weight (molar mass dispersity < 1.03) were successfully synthesized by the living polymerization of phenylacetylene derivatives with a Rh-based multicomponent catalyst system comprising trifunctional initiators, which have three phenylboronates centered on a benzene ring, the Rh complex [Rh(nbd)Cl]2, diphenylacetylene, triphenylphosphine, and a base. The analysis of chiroptical properties of the optically active star polymers obtained by the living polymerization of optically active phenylacetylene derivatives revealed that the star polymers exhibited chiral amplification properties owing to their unique topology compared with the corresponding linear polymers.

Morphological Changes of Polymer-Grafted Nanocellulose during a Drying Process.

Nanocellulose is emerging as a sustainable building block in materials science. Surface modification via polymer grafting has proven to be effective in tuning diverse material properties of nanocellulose, including wettability of films and the reinforcement effect in polymer matrices. Despite its widespread use in various environments, the structure of a single polymer-grafted nanocellulose remains poorly understood. Here, we investigate the morphologies of polymer-grafted CNFs at water-mica and air-mica interfaces by using all-atom molecular dynamics simulation and atomic force microscopy. We show that the morphologies of the polymer-grafted CNFs undergo a marked change in response to the surrounding environment due to variations in the conformation of the surface polymer chains. Our results provide novel insights into the molecular structure of polymer-grafted CNFs and can facilitate the design and development of innovative biomass-based nanomaterials.

Biophysical Properties of the Fibril Structure of the Toxic Conformer of Amyloid-ß42: Characterization by Atomic Force Microscopy in Liquid and Molecular Docking.

Alzheimer's disease is associated with the aggregation of the misfolded neuronal peptide, amyloid-ß42 (Aß42). Evidence has suggested that several reasons are responsible for the toxicity caused by the aggregation of Aß42, including the conformational restriction of Aß42. In this study, one of the toxic conformers of Aß42, which contains a Glu-to-Pro substitution (E22P-Aß42), was explored using atomic force microscopy and molecular docking to study the aggregation dynamics. We proposed a systematic model of fibril formation to better understand the molecular basis of conformational transitions in the Aß42 species. Our results demonstrated the formation of amorphous aggregates in E22P-Aß42 that are stem-based, network-like structures, while the formation of mature fibrils occurred in the less toxic conformer of Aß42, E22-Aß42, that are sphere-like flexible structures. A comparison was made between the biophysical properties of E22P-Aß42 and E22-Aß42 that revealed that E22P-Aß42 had greater stiffness, dihedral angle, number of ß sheets involved, and elasticity, compared with E22-Aß42. These findings will have considerable implications toward our understanding of the structural basis of the toxicity caused by conformational diversity in Aß42 species.

Molecular Dynamics of Drying-Induced Structural Transformations in a Single Nanocellulose.

Nanocellulose is attracting attention in the field of materials science as a sustainable building block. Nanocellulose-based materials, such as films, membranes, and foams, are fabricated by drying colloidal dispersions. However, little is known about how the structure of a single nanocellulose changes during the complex drying process. Here, all-atom molecular dynamics simulations and atomic force microscopy is used to investigate the structural dynamics of single nanocellulose during drying. It is found that the twist morphology of the nanocellulose became localized along the fibril axis during the final stage of the drying process. Moreover, it is shown that conformational changes at C6 hydroxymethyl groups and glycoside bond is accompanied by the twist localization, indicating that the increase in the crystallinity occurred in the process. It is expected that the results will provide molecular insights into nanocellulose structures in material processing, which is helpful for the design of materials with advanced functionalities.

Molecular Assembly and Gelating Behavior of (l)-Alanine Derivatives.

In this study, a low-molecular-weight organogelator derived from (l)-amino acids was designed and synthesized. Gelation assays using (l)-amino acid derivatives were performed to confirm the gelation ability, which was found to be high in several compounds. The (l)-alanine derivatives were determined to be excellent gelators, forming good gels even when smaller amounts were added. These results led to a library of amino acid-derived organogelators. In addition, the thermal properties of the (l)-alanine derivatives with high gelation performance were measured. Differential scanning calorimetry measurements revealed that the thermal stability of the gels could be controlled by changing the gelator concentration. The surface states of the obtained gels were observed by field-emission scanning electron microscopy and atomic force microscopy measurements, which confirmed the structure of the self-molecular aggregates. Self-molecular aggregates were observed to be helical or sheet-like, and the gels were constructed by forming aggregates by self-molecular recognition.

Molecular Scale Structure and Kinetics of Layer-by-Layer Peptide Self-Organization at Atomically Flat Solid Surfaces.

Understanding the mechanisms of self-organization of short peptides into two- and three-dimensional architectures are of great interest in the formation of crystalline biomolecular systems and their practical applications. Since the assembly is a dynamic process, the study of structural development is challenging at the submolecular dimensions continuously across an adequate time scale in the natural biological environment, in addition to the complexities stemming from the labile molecular structures of short peptides. Self-organization of solid binding peptides on surfaces offers prospects to overcome these challenges. Here we use a graphite binding dodecapeptide, GrBP5, and record its self-organization process of the first two layers on highly oriented pyrolytic graphite surface in an aqueous solution by using frequency modulation atomic force microscopy in situ. The observations suggest that the first layer forms homogeneously, generating self-organized crystals with a lattice structure in contact with the underlying graphite. The second layer formation is mostly heterogeneous, triggered by the crystalline defects on the first layer, growing row-by-row establishing nominally diverse biomolecular self-organized structures with transient crystalline phases. The assembly is highly dependent on the peptide concentration, with the nucleation being high in high molecular concentrations, e.g., >100 µM, while the domain size is small, with an increase in the growth rate that gradually slows down. Self-assembled peptide crystals are composed of either singlets or doublets establishing P1 and P2 oblique lattices, respectively, each commensurate with the underlying graphite lattice with chiral crystal relations. This work provides insights into the surface behavior of short peptides on solids and offers quantitative guidance toward elucidating molecular mechanisms of self-assembly helping in the scientific understanding and construction of coherent bio/nano hybrid interfaces.

Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II.

We report a case in which sub-stoichiometric binding of an actin-binding protein has profound structural and functional consequences, providing an insight into the fundamental properties of actin regulation. Rng2 is an IQGAP contained in contractile rings in the fission yeast Schizosaccharomyces pombe Here, we used high-speed atomic force microscopy and electron microscopy and found that sub-stoichiometric binding of the calponin-homology actin-binding domain of Rng2 (Rng2CHD) induces global structural changes in skeletal muscle actin filaments, including shortening of the filament helical pitch. Sub-stoichiometric binding of Rng2CHD also reduced the affinity between actin filaments and muscle myosin II carrying ADP and strongly inhibited the motility of actin filaments on myosin II in vitro. On skeletal muscle myosin II-coated surfaces, Rng2CHD stopped the actin movements at a binding ratio of 11%. Rng2CHD also inhibited actin movements on myosin II of the amoeba Dictyostelium, but in this case, by detaching actin filaments from myosin II-coated surfaces. Thus, sparsely bound Rng2CHD induces apparently cooperative structural changes in actin filaments and inhibits force generation by actomyosin II.

Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy.

Cellulose, a renewable structural biopolymer, is ubiquitous in nature and is the basic reinforcement component of the natural hierarchical structures of living plants, bacteria, and tunicates. However, a detailed picture of the crystalline cellulose surface at the molecular level is still unavailable. Here, using atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we revealed the molecular details of the cellulose chain arrangements on the surfaces of individual cellulose nanocrystals (CNCs) in water. Furthermore, we visualized the three-dimensional (3D) local arrangement of water molecules near the CNC surface using 3D AFM. AFM experiments and MD simulations showed anisotropic water structuring, as determined by the surface topologies and exposed chemical moieties. These findings provide important insights into our understanding of the interfacial interactions between CNCs and water at the molecular level. This may allow the establishment of the structure-property relationship of CNCs extracted from various biomass sources.

Probing the Structural Details of Chitin Nanocrystal-Water Interfaces by Three-Dimensional Atomic Force Microscopy.

Chitin is one of the most abundant and renewable natural biopolymers. It exists in the form of crystalline microfibrils and is the basic structural building block of many biological materials. Its surface crystalline structure is yet to be reported at the molecular level. Herein, atomic force microscopy (AFM) in combination with molecular dynamics simulations reveals the molecular-scale structural details of the chitin nanocrystal (chitin NC)-water interface. High-resolution AFM images reveal the molecular details of chitin chain arrangements at the surfaces of individual chitin NCs, showing highly ordered, stable crystalline structures almost free of structural defects or disorder. 3D-AFM measurements with submolecular spatial resolution demonstrate that chitin NC surfaces interact strongly with interfacial water molecules creating stable, well-ordered hydration layers. Inhomogeneous encapsulation of the underlying chitin substrate by these hydration layers reflects the chitin NCs' multifaceted surface character with different chain arrangements and molecular packing. These findings provide important insights into chitin NC structures at the molecular level, which is critical for developing the properties of chitin-based nanomaterials. Furthermore, these results will contribute to a better understanding of the chemical and enzymatic hydrolysis of chitin and other native polysaccharides, which is also essential for the enzymatic conversion of biomass.

Visualisation of helical structures of poly(diphenylacetylene)s bearing chiral amide pendants by atomic force microscopy.

The helical structures of poly(diphenylacetylene)s bearing optically active substituents linked through amide bonds and with a helicity memory have been visualised using atomic force microscopy. The polymers self-assembled into an ordered 2D monolayer on highly oriented pyrolytic graphite upon exposure to solvent vapour, whose helical pitch and handedness (right- and left-handed) were for the first time directly revealed at molecular resolution.

Structural and mechanical characteristics of exosomes from osteosarcoma cells explored by 3D-atomic force microscopy.

Exosomes have recently gained interest as mediators of cell-to-cell communication and as potential biomarkers for cancer and other diseases. They also have potential as nanocarriers for drug delivery systems. Therefore, detailed structural, molecular, and biomechanical characterization of exosomes is of great importance for developing methods to detect and identify the changes associated with the presence of cancer and other diseases. Here, we employed three-dimensional atomic force microscopy (3D-AFM) to reveal the structural and nanomechanical properties of exosomes at high spatial resolution in physiologically relevant conditions. The substructural details of exosomes released from three different cell types were determined based on 3D-AFM force mapping. The resulting analysis revealed the presence of distinct local domains bulging out from the exosome surfaces, which were associated with the exosomal membrane proteins present on the outer surface. The nanomechanical properties of individual exosomes were determined from the 3D-force maps. We found a considerably high elastic modulus, ranging from 50 to 350 MPa, as compared to that obtained for synthetic liposomes. Moreover, malignancy-dependent changes in the exosome mechanical properties were revealed by comparing metastatic and nonmetastatic tumor cell-derived exosomes. We found a clear difference in their Young's modulus values, suggesting differences in their protein profiles and other exosomal contents. Exosomes derived from a highly aggressive and metastatic k-ras-activated human osteosarcoma (OS) cell line (143B) showed a higher Young's modulus than that derived from a nonaggressive and nonmetastatic k-ras-wildtype human OS cell line (HOS). The increased elastic modulus of the 143B cell-derived exosomes was ascribed to the presence of abundant specific proteins responsible for elastic fiber formation as determined by mass spectroscopy and confirmed by western blotting and ELISA. Therefore, we conclude that exosomes derived from metastatic tumor cells carry an exclusive protein content that differs from their nonmetastatic counterparts, and thus they exhibit different mechanical characteristics. Discrimination between metastatic and nonmetastatic malignant cell-derived exosomes would be of great importance for studying exosome biological functions and using them as diagnostic biomarkers for various tumor types. Our findings further suggest that metastatic tumor cells release exosomes that express increased levels of elastic fiber-associated proteins to preserve their softness.

Photothermal excitation efficiency enhancement of cantilevers by electron beam deposition of amorphous carbon thin films.

In recent years, the atomic force microscope has proven to be a powerful tool for studying biological systems, mainly for its capability to measure in liquids with nanoscale resolution. Measuring tissues, cells or proteins in their physiological conditions gives us access to valuable information about their real 'in vivo' structure, dynamics and functionality which could then fuel disruptive medical and biological applications. The main problem faced by the atomic force microscope when working in liquid environments is the difficulty to generate clear cantilever resonance spectra, essential for stable operation and for high resolution imaging. Photothermal actuation overcomes this problem, as it generates clear resonance spectra free from spurious peaks. However, relatively high laser powers are required to achieve the desired cantilever oscillation amplitude, which could potentially damage biological samples. In this study, we demonstrate that the photothermal excitation efficiency can be enhanced by coating the cantilever with a thin amorphous carbon layer to increase the heat absorption from the laser, reducing the required excitation laser power and minimizing the damage to biological samples.

The local electronic properties of individual Pt atoms adsorbed on TiO2(110) studied by Kelvin probe force microscopy and first-principles simulations.

Noble metal nanostructures dispersed on metal oxide surfaces have applications in diverse areas such as catalysis, chemical sensing, and energy harvesting. Their reactivity, chemical selectivity, stability, and light absorption properties are controlled by the interactions at the metal/oxide interface. Single-atom metal adsorbates on the rutile TiO2(110)-(1 × 1) surface have become a paradigmatic model to characterize those interactions and to understand the unique electronic properties of these supported nanostructures. We combine Kelvin probe force microscopy (KPFM) experiments and density functional theory (DFT) calculations to investigate the atomic-scale variations in the contact potential difference of individual Pt atoms adsorbed on a hydroxylated (h) TiO2(110)-(1 × 1) surface. Our experiments show a significant drop in the local contact potential difference (LCPD) over Pt atoms with respect to the TiO2 surface, supporting the presence of an electron transfer from the Pt adsorbates to the substrate. We have identified two characteristic regimes by LCPD spectroscopy. At far tip-sample distances, LCPD values show a weak distance dependence and can be attributed to the intrinsic charge transfer from Pt to the oxide support. Beyond the onset of short-range chemical interactions, LCPD values exhibit a strong distance dependence that we ascribe to the local structural and charge rearrangements induced by the tip-sample interaction. These findings also apply to other electropositive adsorbates such as potassium and the hydrogen atoms forming the OH groups that are present on the h-TiO2(110) surface, promoting KPFM as a suitable tool for the understanding of electron transfer in catalytically active materials.

Effects of Pb Intercalation on the Structural and Electronic Properties of Epitaxial Graphene on SiC.

The effects of Pb intercalation on the structural and electronic properties of epitaxial single-layer graphene grown on SiC(0001) substrate are investigated using scanning tunneling microscopy (STM), noncontact atomic force microscopy, Kelvin probe force microscopy (KPFM), X-ray photoelectron spectroscopy, and angle-resolved photoemission spectroscopy (ARPES) methods. The STM results show the formation of an ordered moiré superstructure pattern induced by Pb atom intercalation underneath the graphene layer. ARPES measurements reveal the presence of two additional linearly dispersing π-bands, providing evidence for the decoupling of the buffer layer from the underlying SiC substrate. Upon Pb intercalation, the Si 2p core level spectra show a signature for the existence of PbSi chemical bonds at the interface region, as manifested in a shift of 1.2 eV of the bulk SiC component toward lower binding energies. The Pb intercalation gives rise to hole-doping of graphene and results in a shift of the Dirac point energy by about 0.1 eV above the Fermi level, as revealed by the ARPES measurements. The KPFM experiments have shown that decoupling of the graphene layer by Pb intercalation is accompanied by a work function increase. The observed increase in the work function is attributed to the suppression of the electron transfer from the SiC substrate to the graphene layer. The Pb intercalated structure is found to be stable in ambient conditions and at high temperatures up to 1250 °C. These results demonstrate that the construction of a graphene-capped Pb/SiC system offers a possibility of tuning the graphene electronic properties and exploring intriguing physical properties such as superconductivity and spintronics.

(2n × 1) Reconstructions of TiO2(011) Revealed by Noncontact Atomic Force Microscopy and Scanning Tunneling Microscopy.

We have used noncontact atomic force microscopy (NC-AFM) and scanning tunneling microscopy (STM) to study the rutile TiO2(011) surface. A series of (2n × 1) reconstructions were observed, including two types of (4 × 1) reconstruction. High-resolution NC-AFM and STM images indicate that the (4 × 1)-α phase has the same structural elements as the more widely reported (2 × 1) reconstruction. An array of analogous higher-order (2n × 1) reconstructions were also observed where n = 3-5. On the other hand, the (4 × 1)-ß reconstruction seems to be a unique structure without higher-order analogues. A model is proposed for this structure that is also based on the (2 × 1) reconstruction but with additional microfacets of {111} character.

Mechanical gate control for atom-by-atom cluster assembly with scanning probe microscopy.

Nanoclusters supported on substrates are of great importance in physics and chemistry as well as in technical applications, such as single-electron transistors and nanocatalysts. The properties of nanoclusters differ significantly from those of either the constituent atoms or the bulk solid, and are highly sensitive to size and chemical composition. Here we propose a novel atom gating technique to assemble various atom clusters composed of a defined number of atoms at room temperature. The present gating operation is based on the transfer of single diffusing atoms among nanospaces governed by gates, which can be opened in response to the chemical interaction force with a scanning probe microscope tip. This method provides an alternative way to create pre-designed atom clusters with different chemical compositions and to evaluate their chemical stabilities, thus enabling investigation into the influence that a single dopant atom incorporated into the host clusters has on a given cluster stability.

Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy.

The effect of tip chemical reactivity on the lateral manipulation of intrinsic Si adatoms toward a vacancy site on a Si(111)-(7 × 7) surface has been investigated by noncontact atomic force microscopy at room temperature. Here we measure the atom-hopping probabilities associated with different manipulation processes as a function of the tip-surface distance by means of constant height scans with chemically different types of tips. The interactions between different tips and Si atoms are evaluated by force spectroscopic measurements. Our results demonstrate that the ability to manipulate Si adatoms depends extremely on the chemical nature of the tip apex and is correlated with the maximal attractive force measured over Si adatoms. We rationalize the observed dependence of the atom manipulation process on tip-apex chemical reactivity by means of density functional theory calculations. The results of these calculations suggest that the ability to reduce the energy barrier associated with the Si adatom movement depends profoundly on tip chemical reactivity and that the level of energy barrier reduction is higher with tips that exhibit high chemical reactivity with Si adatoms. The results of this study provide a better way to control the efficiency of the atomic manipulation process for chemisorption systems.

Amplitude and frequency modulation torsional resonance mode atomic force microscopy of a mineral surface.

Scanning probe imaging in a shear force mode allows for the characterization of in-plane surface properties. In a standard AFM, shear force imaging can be realized by the torsional resonance mode. In order to investigate the imaging conditions on mineral surfaces, a torsional resonance mode atomic force microscope was operated in amplitude (AM) and frequency modulation (FM) feedback. Freshly cleaved chlorite was investigated, which showed brucite-like and talc-like surface areas. In constant amplitude FM mode, a slight variation in energy dissipation was observed between both surfaces. Amplitude and frequency vs. distance curves revealed that the tip was in repulsive contact with the specimen during imaging.