Pyrolytic Graphite Surface Research Articles

Incorporation of phenylcarbonyl groups in the sidechain: A tool to induce ordered assembly of peptides on surfaces.

The possibility of introducing various functionalities on peptides with relative ease allows them to be used for molecular applications. However, oligopeptides prepared entirely from proteinogenic amino acids seldom assemble as ordered structures on surfaces. Therefore, sidechain modifications of peptides that can increase the intermolecular interactions without altering the constitution of a given peptide become an attractive route to self-assembling them on surfaces. We find that replacing phenylalanine residues with unusual amino acids that have phenylcarbonyl sidechains in oligopeptides increases the formation of ordered self-assembly on a highly ordered pyrolytic graphite surface. Peptides containing the modified amino acids provided extended long-range ordered assemblies, while the analogous peptides containing phenylalanine residues failed to form long-range assemblies. X-ray crystallographic analysis of the bulk structures of these peptides and the analogous peptides containing phenylalanine residues reveal that such modifications do not alter the secondary structure in crystals. It also reveals that the secondary hydrogen bonding interaction through phenylcarbonyl sidechains facilitates extended growth of the peptides on graphite.

Coupling effect of gas solubility in a solvent and substrate structure on performance in nanobubble morphological changes

The distribution morphologies of nanobubbles on Highly Oriented Pyrolytic Graphite (HOPG) surfaces prepared using the alcohol-water exchange test method were observed using atomic force microscopy. In situ observation revealed the distinct growth evolution behavior of nanobubble morphology. Molecular dynamics simulation was employed to replicate the experimental test and investigate the influence of the coupling effect of gas solubility and substrate structure on the morphological features of nanobubble distribution in alcohol-water exchange experiments. The results demonstrate that gas solubility plays a pivotal role in the nucleation of surface nanobubbles during alcohol-water exchange. Specifically, stable surface nanobubbles form only when the solubility exceeds 0.02535. Furthermore, under conditions where gas solubility satisfies the nucleation criteria, the surface potential energy of concave and defective structures exhibits concave characteristics, giving rise to the nucleation of cap-shaped nanobubbles. In contrast, the step structure, characterized by the smallest average surface potential energy, results in relatively flat properties in the lowest area, with nanobubble nucleation taking the form of layer-shaped features. yields relatively uniform characteristics at the lowest level, where nanobubble nucleation manifests in the form of layered features. As time progresses, cap-shaped nanobubbles coalesce, leading to the escape of gas molecules and subsequent dissipation, whereas the layer-shaped nanobubbles adsorb gas molecules from the solution, prompting their expansion.

Characterizing the surface compositions of supported bimetallic PtSn clusters: Effects of cluster-support interactions and surface adsorbates

PtSn bimetallic clusters on TiO2(110) and highly oriented pyrolytic graphite (HOPG) surfaces have been characterized by scanning tunneling microscopy, low energy ion scattering (LEIS), X-ray photoelectron spectroscopy, and temperature programmed desorption (TPD); density functional theory (DFT) calculations have also been performed to better understand adsorption of CO and D2 on the PtSn surfaces. On TiO2 at coverages of 2 ML of Pt and 2 ML of Sn, exclusively bimetallic clusters are formed for both orders of deposition because clusters of the first metal completely cover the surface such that all atoms of the second metal are incorporated into the existing clusters. In contrast, on HOPG, the high mobility and weak cluster-support interactions on HOPG result in much larger 2 ML monometallic clusters (∼30 Å high) that do not completely cover the surface, and deposition of the second metal produces larger clusters as well as smaller ones. Despite the difference in cluster morphologies for the different orders of deposition and supports, the LEIS experiments demonstrate that in all cases, the PtSn clusters are rich in Sn at the surface, as expected based on the lower surface free energy for Sn compared to Pt. Furthermore, the +0.2 eV shift in the Sn(3d5/2) binding energy observed on all surfaces in the presence of Pt is consistent with PtSn alloy formation. Deposition of 2 ML of Sn on TiO2 produces two-dimensional clusters with oxidation of Sn and reduction of titania at the cluster-support interface, but addition of Pt to the Sn clusters causes Sn to diffuse away from this interface, leaving Sn in the metallic state. TPD experiments on 2 ML Pt/TiO2 with increasing coverages of Sn show that the number of adsorption sites for D2 sharply decreases to nearly zero at 0.5 ML, while CO adsorption decreases to zero only at much higher Sn coverages of 2 ML. DFT studies for Sn modified Pt surfaces and bulk structures demonstrate that for CO adsorption at low Sn coverages (≤0.25 ML), the strong Pt-CO interactions induce diffusion of Pt to the cluster surface and the formation of a bulk Pt3Sn alloy, whereas D2 adsorption does not lead to interactions with the Pt surface that are strong enough to induce alloy formation. A single Sn adatom prevents D2 adsorption on four neighboring Pt atoms via site-blocking and the donation of electron density to Pt.

Microscopic growth of pyridinium oxime based amphipathic on graphite: Effect of relative position of substituents

AbstractAmphipathic molecules with surfactant like properties have several applications ranging from healthcare to the chemical industry. Their ability to form thin films on surfaces with ordered and controllable patterns determines their applicability. Here, we report two pyridinium oxime‐based surfactants, which possess similar aggregation properties in solution, but exhibit substantially different assembly on highly oriented pyrolytic graphite (HOPG) surface. The two compounds are regioisomers with the oxime unit placed either in meta or para position of the pyridinium ring. While the para isomer assembled to anisotropic one‐dimensional (1D) islands and long rod‐like structures, the meta isomer formed two‐dimensional (2D) islands on the HOPG surface. This difference is rationalized through molecular level force‐field calculations that show anisotropy in the growth of the para isomer resulting from an effective overlap of the alkyl chains and oxime groups, which is distinctly not feasible in the assembly of the meta isomer. The assembly of these compounds is compared with another oxime‐containing compound of similar structure, but without the charged pyridinium unit. The charged unit seems to be crucial for the preferential formation of multilayer islands even at low coverage.

Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface

Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N′-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may “freeze” DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a “kinetic trapping” mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.

Toward a Comprehensive Understanding of the Anomalously Small Contact Angle of Surface Nanobubbles.

Experimental studies have demonstrated that the gas phase contact angle (CA) of a surface nanobubble (SNB) is much smaller than that of a macroscopic gas bubble. This reduced CA plays a crucial role in prolonging the lifetime of SNBs by lowering the bubble pressure and preventing gas molecules from dissolving in the surrounding liquids. Despite extensive efforts to explain the anomalously small CA, a consensus about the underlying reasons is yet to be reached. In this study, we conducted experimental investigations to explore the influence of gas molecules adsorbed at the solid-liquid interface on the CA of SNBs created through the solvent exchange (SE) method and temperature difference (TD). Interestingly, no significant change is observed in the CA of SNBs on highly oriented pyrolytic graphite (HOPG) surfaces. Even for nanobubbles on micro/nano pancakes, the CA only exhibited a slight reduction compared to SNBs on bare HOPG surfaces. These findings suggest that gas adsorption at the immersed solid surface may not be the primary factor contributing to the small CA of the SNBs. Furthermore, the CA of SNBs formed on polystyrene (PS) and octadecyltrichlorosilane (OTS) substrates was also investigated, and a considerable increase in CA was observed. In addition, the effects of other factors including impurity, electric double layer (EDL) line tension, and pinning force upon the CA of SNBs were discussed, and a comprehensive model about multiple factors affecting the CA of SNBs was proposed, which is helpful for understanding the abnormally small CA and the stability of SNBs.

FPGA and computer-vision-based atom tracking technology for scanning probe microscopy

Atom tracking technology enhanced with innovative algorithms has been implemented in this study, utilizing a comprehensive suite of controllers and software independently developed domestically. Leveraging an on-board field-programmable gate array (FPGA) with a core frequency of 100 MHz, our system facilitates reading and writing operations across 16 channels, performing discrete incremental proportional-integral-derivative (PID) calculations within 3.4 microseconds. Building upon this foundation, gradient and extremum algorithms are further integrated, incorporating circular and spiral scanning modes with a horizontal movement accuracy of 0.38 pm. This integration enhances the real-time performance and significantly increases the accuracy of atom tracking. Atom tracking achieves an equivalent precision of at least 142 pm on a highly oriented pyrolytic graphite (HOPG) surface under room temperature atmospheric conditions. Through applying computer vision and image processing algorithms, atom tracking can be used when scanning a large area. The techniques primarily consist of two algorithms: the region of interest (ROI)-based feature matching algorithm, which achieves 97.92% accuracy, and the feature description-based matching algorithm, with an impressive 99.99% accuracy. Both implementation approaches have been tested for scanner drift measurements, and these technologies are scalable and applicable in various domains of scanning probe microscopy with broad application prospects in the field of nanoengineering.

Optimizing the methodology for accurate and accessible slip length measurement with atomic force microscopy

The remarkable performance of cooling devices employing nano- and microscale channels has drawn considerable interest, highlighting the need for surfaces with large slip lengths to improve their efficiency. However, the large errors in slip length associated with existing techniques hinder a clear understanding of slip phenomena. In this paper, we evaluate existing analytical methods for slip length measurement with atomic force microscopy (AFM) and propose a new reliable method. We performed force curve measurements on mica, silica and highly ordered pyrolytic graphite surfaces in water using an AFM equipped with a colloidal probe. The obtained force curves were analyzed through three methods: two commonly utilized procedures, namely the recursive and intercept methods, and a novel one called the two-parameter method which we developed. Our analyses showed that the recursive method yielded slip lengths with relatively large errors, fluctuation of ±5.8 nm, which were due to inaccuracies in the cantilever's spring constant and the fluid viscosity. On the other hand, it was found that the intercept method leads to restrictions on the choice of fitting range because of the simplified formula for viscous drag. As a result, by altering the data range, the calculated slip length shows significant variations within the ranges of ±27.5 nm. The two-parameter method, unlike the standard ones, overcome these drawbacks. This method requires no pre-measured parameters, and the slip length fluctuation is independent of the fitting range and only ±3.6 nm, which is around 2/3 of that observed in the recursive method and 1/8 of that in the intercept method. Our study optimizes existing analytical protocols and offers a new way for accessible and reliable calculations of slip lengths.

Effect of Highly Ordered Pyrolytic Graphite Surfaces on the Production of H⁻ Negative Ions in ECR–Driven Plasmas

Effect of Highly Ordered Pyrolytic Graphite Surfaces on the Production of H⁻ Negative Ions in ECR–Driven Plasmas

Nano-protrusions in intercalated graphite: understanding the structural and electronic effects through DFT.

Complex phenomena characterize the intercalation of ions inside stratified crystals. Their comprehension is crucial in view of exploiting the intercalation mechanism to change the transport properties of the crystal or obtaining a fine control of crystal delamination. In particular, the relationship between the concentration and nature of intercalated ions and surface structural modifications of the host stratified crystal is still under debate. Here, we discuss a theoretical effort to provide a rationale for some structural changes observed on the highly oriented pyrolytic graphite (HOPG) surface after electrochemical treatment in perchloric and sulphuric acid solutions. The formation of the so-called nano-protrusions on the basal plane of intercalated graphite was previously observed with scanning tunneling microscopy (STM). In this work, we employed both STM and density functional theory (DFT) simulations to elucidate the physical and chemical mechanisms driving the emergence of these nano-protrusions. The DFT results show that, in a bilayer graphene system, the presence of a single ion can generate a nano-protrusion with 2.49 Å height and 21.27 Å width. In the deformed area, the C-C bond length is stretched by about 2.5% more than the normal graphene bond. These values are of the same dimensional scale as those reported in previous STM experimental results.25 However, the simulated STM images obtained by increasing the amount of intercalated ions per area suggest that the presence of more than one ion is needed for the deformation of the uppermost graphite layer during the early stages of intercalation. In contrast, in a multilayer graphene system, no significant surface deformation is detected when ions are intercalated between the third and fourth layers. Charge analysis indicates an altered distribution of the charges as a consequence of the intercalation. The charge transfer from graphene layers to the intercalated ions results in a surface layer more prone to oxidation.

Phospholipid Epitaxial Assembly Behavior on a Hydrophobic Highly Ordered Pyrolytic Graphite Surface.

Supported lipid bilayers (SLBs) are excellent models of cell membranes. However, most SLBs exist in the form of phospholipid molecules standing on a substrate, making it difficult to have a side view of the phospholipid membranes. In this study, the phospholipid striped lamella with the arrangement of their alkane tails lying on highly ordered pyrolytic graphite (HOPG) was constructed by a spin coating method. Atomic force microscopy and molecular dynamics simulations are utilized to study the self-assembly of phospholipids on HOPG. Results show that various phospholipids with different packing parameters and electrical property are able to epitaxially adsorb on HOPG. 0.1 mg/mL Plasm PC (0.1 mg/mL) could form a striped monolayer with a width of 5.93 ± 0.21 nm and form relatively stable four striped layers with the concentration increasing to 1 mg/mL. The width of the DOPS multilayer is more than that of electroneutral lipids due to the static electrical repulsion force. This universal strategy sheds light on direct observation of the membrane structure from the side view and modification of 2D materials with amphiphilic biomolecules.

Low friction under ultrahigh contact pressure enabled by self-assembled fluorinated azobenzene layers

Extensive efforts have been made to pursue a low-friction state with promising applications in many fields, such as mechanical and biomedical engineering. Among which, the load capacity of the low-friction state has been considered to be crucial for industrial applications. Here, we report a low friction under ultrahigh contact pressure by building a novel self-assembled fluorinated azobenzene layer on an atomically smooth highly-oriented pyrolytic graphite (HOPG) surface. Sliding friction coefficients could be as low as 0.0005 or even lower under a contact pressure of up to 4 GPa. It demonstrates that the low friction under ultrahigh contact pressure is attributed to molecular fluorination. The fluorination leads to effective and robust lubrication between the tip and the self-assembled layer and enhances tighter rigidity which can reduce the stress concentration in the substrate, which was verified by density functional theory (DFT) and molecular dynamics (MD) simulation. This work provides a new approach to avoid the failure of ultralow friction coefficient under relatively high contact pressure, which has promising potential application value in the future.

The regulation of surface nanobubble generation via solvent exchange on different substrates

Surface nanobubbles (SNBs) play an essential role in fluid transport, interfacial reactions, electrochemistry, material fabrication, surface cleaning, etc. Controllable preparation of SNBs is very crucial for their applications, such as controlling material preparation and increasing the efficiency of surface cleaning. Ethanol-water exchange, as a typical example of solvent exchange, is one of the most widely used methods to produce SNBs. By controlling the conditions, it is possible to manipulate the size and number density of nanobubbles. In this work, we systematically investigated the formation of SNBs on hydrophobic and hydrophilic surfaces by ethanol-water exchange at different rates using atomic force microscopy. Results indicate that the exchange rate has a significant effect on the size and number density of SNBs. On both hydrophobic surface of highly oriented pyrolytic graphite (HOPG) and hydrophilic surface of mica, formed nanobubbles exhibit smaller sizes and higher number density with increased exchange rates. But at the same solvent exchange rate, SNBs generated on HOPG surface were in greater number and width than on mica, while their heights change much less. To understand the effect of exchange rate on nanobubble production, we proposed a mechanism of non-uniform nucleation and diffusion-driven growth. A simulation of the gas concentration near SNBs was performed, and the results show good agreement between numerical calculations and experimental data. We believe that our results will contribute to the understanding of nanobubble generation and stabilization processes. It also provides a new perspective on the factors that affect the generation of SNBs, which allows the production and application of nanobubbles to be controlled in a reliable manner.

Gas concentration in rarefied flows: Experiments and modeling

The relationship between gas-surface scattering dynamics and flow through conical systems in the rarefied regime has been explored with experimental and computational tools. Molecular beam-surface scattering experiments were used to characterize the inelastic scattering dynamics of Ar and N2 on a highly oriented pyrolytic graphite (HOPG) surface. These data were then used to develop a gas-surface scattering approach for kinetic fluid simulations, which combines the diffuse scattering and Cercignani-Lampis-Lord (CLL) models. The translational energy and angular flux distributions from the beam-surface scattering experiments were used to obtain the normal energy accommodation (αn) parameter as well as the effective surface mass (M) in the CLL model. Constant values of αn=0.9, M = 40 amu for Ar and αn=0.75, M = 28 amu for N2 were found to capture the experimental angular flux scattering distributions over a wide range of incident energies and angles. The gas-surface model was subsequently used in direct simulation Monte Carlo (DSMC) simulations of the flux of directed gas flow through a conical concentrator and compared with measurements of gas concentration with a prototype concentrator in separate molecular beam experiments. Comparisons of predicted concentration pressure ratios (pressure in an accommodation chamber with vs. without concentrator) with measured values for three free-stream velocities of Ar and N2 showed maximum deviations of 4.8% and 9.8% for Ar and N2, respectively. The simulations show that gas-surface collisions resulting in the loss of the normal component of the incident energy while preserving the tangential momentum of the impinging atom or molecule, resulting in super-specular scattering, lead to higher concentration of gases than purely specular, energy conserving gas-surface interactions. For conical concentrators, with inlet-to-outlet area ratios of 133 and 600, specular reflections result in concentration factors (flux through an orifice with vs. without concentrator) of only ∼8, while super-specular scattering results in concentration factors of 64 and 127, respectively.

Anisotropy of nanoscale friction: Influence of lattice structure, temperature, and wear

The anisotropy of nanoscale friction is analyzed for different samples using friction force microscopy under ultrahigh-vacuum conditions with varying scan directions. For both $\mathrm{Mo}{\mathrm{S}}_{2}$ and highly oriented pyrolytic graphite surfaces, our experiments reveal a sixfold symmetry of the friction vector plots in accordance with solutions of the Langevin equation, where the atomic force microscope tip is treated as a point mass elastically driven on the hexagonal surface lattices. In addition, the effect of temperature is analyzed both by experiment and by simulations. In both cases we find that increased temperature not only lowers the absolute friction values but also decreases the friction anisotropy. In contrast, experiments on NaCl cannot be explained on a similar basis. While the square symmetry is clearly revealed in the first measurements, it progressively deteriorates with repeated scanning, which is possibly due to abrasive wear occurring at the interface.

Reversible Tuning of Surface Properties of Graphene-like Material via Covalently Functionalized Hydrophobic Layer

Nanoscale tuning of the surface properties of graphene-like materials is essential to optimize their application in electronic devices and protective technologies. The covalent modification method has recently been established as the most effective approach for tailoring the interface structure and properties, which are key aspects for fine-tuning the processability and performance of graphene-like materials. In this work, we demonstrate systematic exploration of the reversible covalent functionalization of a highly oriented pyrolytic graphite (HOPG) surface, a model system of multi-layered graphene, at the molecular scale. This is achieved using 3,5-trifluoromethyl benzenediazonum (3,5-TFD) and experimental investigations via cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), scanning tunneling microscopy (STM), and Raman spectroscopy. The degree of functionalization could be tuned by varying the concentration of 3,5-TFD dissolved in the grafting electrolyte. The covalently functionalized layer of 3,5-TFD was either locally degrafted by the STM tip or globally detracted upon thermal treatment, leaving the defect-free graphitic surfaces behind. Our findings open a new pathway for reversibly and robustly functionalizing graphene and other 2D materials for multiple uses in high-end applications.

In-situ imaging of the electrode surface during electrochemical reactions with a beetle-type electrochemical scanning tunneling microscope

In this paper, we present the design and performances of a beetle-type electrochemical scanning tunneling microscope (EC-STM) which allows horizontal tip motion at millimeter range (5 mm × 5 mm). With its symmetrical scanner design inducing a relatively low thermal drift, the beetle-type EC-STM has the desirable ability to operate in a variety of chemical reactions. Atom-resolved high-resolution STM images of highly oriented pyrolytic graphite (HOPG) and Au(111) surfaces in the liquid phase are presented to confirm the scan performance of the beetle-type EC-STM, which also provides in situ information on the electrode surface during electrochemical reactions, including adsorbed– and desorbed– electrolyte and metal electrodeposition. These systemically obtained STM images on the electrode surface clearly demonstrate the high stability of the newly developed EC‐STM under reaction conditions.

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.

Molecular Resolution Nanostructure and Dynamics of the Deep Eutectic Solvent-Graphite Interface as a Function of Potential.

Interest in deep eutectic solvents (DESs), particularly for electrochemical applications, has boomed in the past decade because they are more versatile than conventional electrolyte solutions and are low cost, renewable, and non-toxic. The molecular scale lateral nanostructures as a function of potential at the solid-liquid interface-critical design parameters for the use of DESs as electrochemical solvents-are yet to be revealed. In this work, in situ amplitude modulated atomic force microscopy complemented by molecular dynamics simulations is used to probe the Stern and near-surface layers of the archetypal and by far most studied DES, 1:2 choline chloride:urea (reline), at the highly orientated pyrolytic graphite surface as a function of potential, to reveal highly ordered lateral nanostructures with unprecedented molecular resolution. This detail allows identification of choline, chloride, and urea in the Stern layer on graphite, and in some cases their orientations. Images obtained after the potential is switched from negative to positive show the dynamics of the Stern layer response, revealing that several minutes are required to reach equilibrium. These results provide valuable insight into the nanostructure and dynamics of DESs at the solid-liquid interface, with implications for the rational design of DESs for interfacial applications.

INTERACTION OF GOLD AND NICKEL NANOPARTICLES WITH MOLECULAR HYDROGEN AND CARBON MONOXIDE IN THE PRESENCE OF AN ELECTRIC FIELD

A nanostructured gold–nickel coating has been synthesized on the surface of pyrolytic graphite. Its physicochemical properties have been studied by scanning tunneling microscopy and spectroscopy, Auger spectroscopy, mass spectrometry, and other methods. It has been found that the coating consists of clusters formed by gold and nickel nanoparticles. It has been shown that an electric field can inhibit or stimulate the adsorption of hydrogen on gold and the reduction of the oxidized surface of nickel nanoparticles with carbon monoxide. The mechanisms of the influence of the field on the chemical processes involving H2 and CO are different. Quantum-chemical simulation has made it possible to determine the values of the energy barriers for CO adsorption on nickel nanoparticles.