Flat Graphite Surface Research Articles

Molecular recognition characteristics of co-assembled peptides on atomically flat graphite surfaces

Molecular recognition, involving the binding of two or more molecules, is widely found in multiple disciplines. It plays a crucial role in driving specific molecular functionalization or biological activities such as antigen–antibody interactions. Recently, the molecular recognition of single peptides self-assembly at interfaces has been widely investigated since their broad applications in biosensors and bioelectronics. However, the recognition characteristics of peptide-peptide co-assembly on solids has not been investigated yet, which provides a basis for potential multi-probes biosensing or structure-intermingled functionalized bioelectronic applications. Here, we explored the molecular recognition characteristics of co-assembled peptides on two-dimensional (2D) layered nanomaterials, specifically graphite. Our findings showed distinct surface characteristics of peptide co-assembly in comparison to the independent peptides self-assembly. Peptide co-assembly exhibited the nucleation and growth heterogeneities with reduced nucleation and growth rates, dominated by a diffusion-limited step as confirmed via carrying out the sequential-assembled experiments. Moreover, molecular dynamics simulation reveals a slowdown binding process of co-assembled peptides to graphite. Furthermore, the misattachment of one peptide to arrays of another types of peptide with distinct structural ordering orientations severely postponed peptide elongation. Therefore, our work provides valuable insight into the fundamental surface characteristics of two co-assembled peptides as they specifically recognize graphite surface via undergoing continuous surface behaviors from binding to diffusion until final ordering process. The formation of co-assembled peptide patterns on 2D layered nanomaterials incorporates multiple functions enabling to provide potential applications in intermingled peptide-based biosensing or bioelectronic nanodevices.

Temperature-dependent friction coefficient on flat graphite plane

Investigating the frictional properties of two-dimensional layered materials with dynamic evolution of contact quality advances understanding the mechanism underlying puckering effects, offering a new pathway for the rational control of friction. In this letter, friction force microscopy (FFM) in ultra-high vacuum (UHV) conditions has been used to probe the nanoscale friction on a freshly cleaved flat graphite surface (0001) as a function of normal force and surface temperature. It is found that friction force shows a nonmonotonic change with the decrease of temperature with the maximum friction appeared around Tmax=140±5 K. Besides, coefficients of friction (COFs) defined as the slope of friction-normal force curves remains nearly constant before the friction peak while surprisingly change into negative values with the further decrease of temperature. The loading–unloading results reveal that, the abnormal COFs behavior originates from the temperature induced contact quality evolution which leads to the ripple formation at cryogenic temperatures in the front of scanning tip. The results reported here provide a deep insight into the effects of temperature on the frictional behaviors of graphite, which give a new thrust in the field of friction on lamellar materials.

About graphite evaporation dynamics caused by radiation in near zone of magnetoplasma compressor discharge

The results of processes above the surface of graphite samples which exposed with powerful vacuum ultraviolet (VUV) radiation experimental studies are presented. The characteristic radiation exposure time was 3...100 μs, the radiation energy in the vacuum region of the spectrum was 1...2 kJ. The main characteristics of the processes were recorded on direct, shadow photographs and interferograms. The temporal dynamics of the expansion of the plasma layer formed during evaporation of the flat graphite targets surface by VUV radiation, as well as the dynamics of buffer gas compression and shock wave motion are analyzed. It is shown that the temperature of the carbon plasma above the samples surface reached 1 eV. Research is relevant in the fields of space, plasma technologies, the development of the element base of microelectronics and fundamental studies of the powerful radiation interaction with matter.

Abnormal retention of s-triazine herbicides on porous graphitic carbon

Abstract Porous graphitic carbon (PGC) is a widely used stationary phase for reversed-phase high-performance liquid chromatography (HPLC) that allows separation of structurally similar compounds retained in mixed form on a flat graphite surface. Such a stationary phase can be used in analytical chemistry to provide good separation and selectivity in pesticide monitoring. In this article, we studied the chromatographic behavior of five common triazine herbicides (simazine, atrazine, desmetryn, propazine, prometryn) on PGC vis-à-vis octadecyl-functionalized silica gel (ODS). It was found that the herbicides studied have an abnormal elution order on PGC compared to ODS. PGC was also characterized by higher selectivity of analyte separation. This behavior of triazine herbicides on PGC cannot be explained either with the help of existing theory or by mathematical modeling of adsorption processes on graphite. Therefore, we have proposed a possible retention mechanism, explaining the effects observed, due to the shielding of the amino group in the triazine ring by alkyl substituents, which decreases the “polar retention effect” of PGC. Satisfactory separation efficacy was obtained with the proposed analytical method, using convenient UV-detection and without resort to laborious techniques such as HPLC coupled with mass spectrometry.

Modeling Enhanced Adsorption of Explosive Molecules on a Hydroxylated Graphene Pore

The possibility of a graphene bilayer nanosensor for the detection of explosive molecules was modeled using computational chemistry. A pore was designed on a graphene bilayer structure with three strategically placed perimeter hydroxyl (OH) groups built around the edge of an indented, two-dimensional hexagonal pore. This hydroxylated pore and models of various explosive molecules were optimized using MM2 molecular mechanics parameters. Values were calculated for the molecule-surface interaction energy (binding energy), E, for 22 explosive molecules on a flat graphene bilayer and on the specially designed hydroxylated pore within the bilayer. The molecule-surface binding energy for trinitrotoluene (TNT) increased from 17.9 kcal/mol on the flat graphene bilayer to 42.3 kcal/mol on the hydroxylated pore. Due to the common functionality of nitro groups that exist on many explosive molecules, the other explosive molecules studied gave similar enhancements based on the specific hydrogen bonding interactions formed within the pore. Each of the 22 explosive adsorbate molecules showed increased molecule-surface interaction on the bilayer hydroxylated pore as compared to the flat bilayer. For the 22 molecules, the average E for the flat graphite surface was 15.8 kcal/mol and for the hydroxylated pore E was 33.8 kcal/mol. An enhancement of adsorption should make a detection device more sensitive. Nanosensors based on a modified graphene surface may be useful for detecting extremely low concentrations of explosive molecules or explosive signature molecules.

Dramatic Nano-Fluidic Properties of Carbon Nanotube Membranes As a Platform for Programmable Transdermal Drug Delivery

Carbon nanotubes (CNT) have three key attributes that make them of great interest for novel membrane applications 1) atomically flat graphite surface allows for ideal fluid slip boundary conditions for 10,000 fold faster fluid flow 2) the cutting process to open CNTs inherently places functional chemistry at CNT core entrance for gatekeeper activity and 3) CNT are electrically conductive allowing for electrochemical reactions and application of electric fields gradients at CNT tips. Pressure driven flux of a variety of solvents (H2O, hexane, decane ethanol, methanol) are 4-5 orders of magnitude higher than conventional Newtonian flow [Nature 2005, 438, 44] due to atomically flat graphite planes inducing nearly ideal slip conditions. However this is eliminated with selective chemical functionalization [ACS Nano 2011 5 3867-3877] needed to give chemical selectivity. These unique properties allow us to explore the hypothesis of producing ‘Gatekeeper’ membranes that mimic natural protein channels. With anionic tip functionality strong electroosmotic flow is induced by unimpeded cation flow with similar 10,000 fold enhancements [Nature Nano 2012 7 133-39]. With enhanced power efficiency, carbon nanotube membranes were employed as the active element of a switchable transdermal drug delivery device that can facilitate more effective treatments of drug abuse and addiction [PNAS . 2010 107 11698]. Due to extremely efficient electroosmosis in the CNT conduits, a watch battery coin cell is able to operate for over 7 days nicotine delivery switching between target dosing of static diffusion transdermal patch and that of nicotine gum. Using optimal fabrication and operational conditions (pH8, -1.5V), ON nicotine fluxes of 5.9 µmoles/cm2/h and ON/OFF ratio of 15 were achieved. This exceeds the demand for nicotine cessation treatment 1.1 µmoles/cm2/h (4mg gum) and ON/OFF ratio (3.6-11) and allows for an active patch area of 4.1cm2, compared to 22cm2 of commercial patches. Power consumption per dose rate of 120 μW/cm2-(μmol/cm2-s) was achieved. Use of electroosmosis in CNTs gives high power efficiencies for compact battery sources. For treatments with a continuous 21mg/24h delivery (commercial patch), a watch battery can last 20.5 days pumping. For early stage treatments with patch and 10x4mg gum dosing, battery life of 7.1 days is expected, well within useful device replacement periods.The systems is demonstrated to work with smart-phone enabled counseling app to form a dosing calendar that is wirelessly transmitted to Bluetooth microcontroller.

Probing the Link among Genomic Cargo, Contact Mechanics, and Nanoindentation in Recombinant Adeno-Associated Virus 2.

Recombinant adeno-associated virus (AAV) is a promising gene therapy vector. To make progress in this direction, the relationship between the characteristics of the genomic cargo and the capsid stability must be understood in detail. The goal of this study is to determine the role of the packaged vector genome in the response of AAV particles to mechanical compression and adhesion to a substrate. Specifically, we used atomic force microscopy to compare the mechanical properties of empty AAV serotype 2 (AAV2) capsids and AAV2 vectors packaging single-stranded DNA or self-complementary DNA. We found that all species underwent partial deformation upon adsorption from buffer on an atomically flat graphite surface. Upon adsorption, a preferred orientation toward the twofold symmetry axis on the capsid, relative to the substrate, was observed. The magnitude of the bias depended on the cargo type, indicating that the interfacial properties may be influenced by cargo. All particles showed a significant relative strain before rupture. Different from interfacial interactions, which were clearly cargo-dependent, the elastic response to directional stress was largely dominated by the capsid properties. Nevertheless, small differences between particles laden with different cargo were measurable; scAAV vectors were the most resilient to external compression. We also show how elastic constant and rupture force data sets can be analyzed according a multivariate conditional probability approach to determine the genome content on the basis of a database of mechanical properties acquired from nanoindentation assays. Implications for understanding how recombinant AAV capsid-genome interactions can affect vector stability and effectiveness of gene therapy applications are discussed.

A study of a nano-sized water droplet’s transition from a flat surface to a pillared surface

The ability to control the hydrophobicity of a surface is of importance to many industries. The dynamic behavior of nano-sized water droplets moving from a flat surface to a pillared surface using molecular dynamics simulations was investigated. Simulations were carried out in two steps. In the first computational step, the initial group of water molecules reached equilibrium on a flat graphite surface. In the second computational step, a constant force was applied to the water droplet and the motion of the water droplet was evaluated as it moved from the flat surface to the pillar-type surface. The movement of the water droplet could be grouped into three different categories and depended on the pillar height and the magnitude of the applied force. The results showed the strongest body force with a pillar height of 6 graphite layers allowed most of the water molecules to move along the top of the pillars. In conclusion, a strong force and pillar height approximately half of the droplet height displayed the best transition from a flat surface to a pillared surface.

Observation of Landau levels on nitrogen-doped flat graphite surfaces without external magnetic fields.

Under perpendicular external magnetic fields, two-dimensional carriers exhibit Landau levels (LLs). However, it has recently been reported that LLs have been observed on graphene and graphite surfaces without external magnetic fields being applied. These anomalous LLs have been ascribed primarily to a strain of graphene sheets, leading to in-plane hopping modulation of electrons. Here, we report the observation of the LLs of massive Dirac fermions on atomically flat areas of a nitrogen-doped graphite surface in the absence of external magnetic fields. The corresponding magnetic fields were estimated to be as much as approximately 100 T. The generation of the LLs at the area with negligible strain can be explained by inequivalent hopping of π electrons that takes place at the perimeter of high-potential domains surrounded by positively charged substituted graphitic-nitrogen atoms.

Label-free sensing of adenosine based on force variations induced by molecular recognition.

We demonstrate a simple force-based label-free strategy for the highly sensitive sensing of adenosine. An adenosine ssDNA aptamer was bound onto an atomic force microscopy (AFM) probe by covalent modification, and the molecular-interface adsorption force between the aptamer and a flat graphite surface was measured by single-molecule force spectroscopy (SMFS). In the presence of adenosine, the molecular recognition between adenosine and the aptamer resulted in the formation of a folded, hairpin-like DNA structure and hence caused a variation of the adsorption force at the graphite/water interface. The sensitive force response to molecular recognition provided an adenosine detection limit in the range of 0.1 to 1 nM. The addition of guanosine, cytidine, and uridine had no significant interference with the sensing of adenosine, indicating a strong selectivity of this sensor architecture. In addition, operational parameters that may affect the sensor, such as loading rate and solution ionic strength, were investigated.

Dynamic hydrophobicity on flat and pillared graphite surfaces with different pillar surface fractions

The motion of a droplet on a surface is of importance to many fields. While many things are known at the macro-scale still a complete understanding of fluid flow at the nano-scale is far from being known. This study focuses on the dynamic hydrophobicity of a pillar surface with different pillar surface fractions at the nano-scale using molecular dynamics simulations. Five pillar heights and four pillar surface fractions were modeled using a graphite surface which has anisotropic characteristics due to its spaced layers. A nano-sized water droplet with 5124 molecules was run to equilibrium on each surface. Then a body force was applied and the dynamic contact angles were calculated for 5 ns. These contact angles were used to calculate the surface’s effective hydrophobicity. The droplets were categorized into one of three groups as different phenomena were identified depending on the pillar surface fraction, applied force, and pillar height. It was found that at the nano-scale smooth, flat surfaces are dynamically more hydrophobic than any of the cases with pillars. Larger pillar surface fractions tended to be more hydrophobic and the pillar surface fraction of 36% was least affected by pillar height and applied body force.

A novel application of kinetic Monte Carlo method in the description of N2 vapour–liquid equilibria and adsorption

We present a novel application of kinetic Monte Carlo (kMC) to describe vapour–liquid equilibria (VLE), vapour–solid equilibria (VSE) and adsorption of nitrogen on a flat graphite surface and in graphitic slit pores. This method is applied, for the first time, to molecules having Lennard-Jones sites and fixed partial charges. For the bulk phase equilibria, we have found that all the thermodynamic properties agree well with experimental data and pre-existing simulations over a wide range of temperatures. A major advantage of the kMC method is its excellent performance under conditions where the Gibbs ensemble simulation fails to achieve convergence, especially in dense phases. Moreover, the calculation of the chemical potential is incorporated in the scheme, which avoids the need for tedious additional procedures, such as the Widom method, required in conventional methods, which add significant computational overheads. For adsorption on a graphite surface, the kMC results are superior to those from a conventional GCMC simulation under conditions where dense phases exist; this is attributed to efficient sampling of the kMC scheme.

Application of the kinetic Monte Carlo method in the microscopic description of argon adsorption on graphite

We present an application of kinetic Monte Carlo (kMC) in the canonical ensemble to a calculation of vapour liquid equilibrium and to describe the adsorption of argon on a flat graphite surface and in a slit-like graphitic pore. Simulations at 77 and 87.3 K accurately describe the experimental data. The kMC method is simple to implement and, unlike conventional Monte Carlo, no rejection trials are necessary. The only move is a uniform sampling of the volume space, which makes the determination of the chemical potential straightforward using real particles in the simulation, in the same spirit as the Widom inverse potential distribution. This avoids the need to freeze the real particles before the trial insertion of test particles as is necessary in other methods, such as the Widom method and its variants.

An immersion calorimetry study of the interaction of organic compounds with carbon nanotube surfaces

The interaction of organic chemicals with the surface of carbon nanotubes (CNTs) has been studied by immersion calorimetry revealing new information about the unique CNT surface structures. The curvature of the graphene sheets of in the CNTs increases the adsorption strength of aromatic compounds compared to flat graphite surfaces. For a given CNT, the adsorption affinity of a non-polar aromatic molecule correlated poorly with the CNT hydrophobicity. Comparison of the immersion enthalpies that evolved when the solids were immersed in organic chemicals reveals the formation of π–π stacking interactions, H-bonds or electron–accepting interactions depending on the CNT surfaces and on the immersion substrate. The number of oxygen groups on CNTs seems to modify the electron density of their surfaces and therefore the interaction mechanism with the adsorbates.

Preparation, structure, and a coarse-grained molecular dynamics model for dodecanethiol-stabilized gold nanoparticles

Thiol-stabilized metal nanoparticles possess unique properties in the comparison with larger-scale materials, which enable their use in many promising chemical and biological applications. We have synthesized thiol-coated colloidal gold nanoparticles (AuNP) soluble in non-polar organic solvents by a simplified procedure, in which AuCl 4 - was initially reduced in aqueous phase and then coated with thiol residues and transferred to organic phase. Using the transmission electron micrograph (TEM) imaging, the average diameter of a dodecanethiol-stabilized AuNP was estimated to be 3.75 ± 0.06 nm. Based on the experimental TEM data, a new coarse-grained molecular dynamics model of AuNP was developed. The model was applied for studying self-assembly of AuNPs on a flat graphite surface, enabling further elucidating the structure and packing of the ligand shell around the spherical nanoparticle core.

Aggregation of Human Serum Albumin on Graphite and Single-Walled Carbon Nanotubes as Studied by Scanning Probe Microscopies

Human serum albumin (HSA) is the most abundant protein in blood plasma showing a remarkable ability to bind a broad range of hydrophobic substrates. We employed scanning tunneling microscopy and atomic force microscopy to characterize the morphology of HSA aggregates on highly-ordered pyrolytic graphite (HOPG) and single-walled carbon nanotubes (SWNTs). The morphologies found for albumin aggregates on HOPG are quite different from the ones observed on SWNTs. On HOPG, HSA forms aggregates of roughly 10-20 molecules; single protein molecules were observed as well. In the case of SWNTs, nanotubes were partially or totally covered with HSA, exhibiting four general types of aggregation: (i) SWNT sidewalls contain single molecules of albumin which are away from each other at distances longer than the HSA molecular size; (ii) SWNTs are completely covered with HSA, which forms a thin and relatively homogeneous layer; (iii) SWNTs have a complete layer of HSA with additional accumulation of protein at separate sites; and (iv) several SWNTs totally covered with albumin assemble into a bundle-like structure common for bare nanotubes. These observations are interpreted in terms of stronger interactions of HSA with nanotube sidewalls than with flat graphite surface.

Effects of confinement on the molar enthalpy of argon adsorption in graphitic cylindrical pores: A grand canonical Monte Carlo (GCMC) simulation study

Using a grand canonical Monte Carlo simulation, we study argon adsorption in graphitic cylindrical pores to investigate the differences between the isosteric heat and the integral molar enthalpy under subcritical and supercritical conditions and compare these results against those for a flat graphite surface to investigate the role of confinement on the enthalpy change of adsorption. The isosteric heat curve is finite under subcritical conditions, but for supercritical adsorption, it becomes infinite at the pressure where the excess concentration versus pressure is maximum. This can be circumvented using the integral molar enthalpy, which is a better variable to describe the energy change for supercritical adsorption. Finally, the effects of pore geometry (radius and length) on argon adsorption under subcritical and supercritical conditions are discussed.

Effects of Surface Curvature and Surface Strength on Argon Adsorption in Carbon Nanotubes at Temperatures below the Triple Point

This paper describes an investigation of argon adsorption into carbon nanotubes at temperatures below the triple point, using a grand canonical Monte Carlo simulation to study the effects of confinement and surface strength on the 2D transition. In large pores, it was found that 2D transitions can occur in more than one layer, but are absent in higher layers for small pores. The 2D critical temperature of the first layer for a small pore (R = 1.2 nm) was found to be ca. 66 K (MWCNT) and 65 K (SWCNT), compared to 55–59 K observed experimentally for a flat graphite surface. This is because of the overlapping effects due to the surface curvature or the confinement in a carbon nanotube. Assuming a weaker carbon surface by reducing the graphene surface strength by 40% for SWCNT, the 2D critical temperature was only modestly reduced to 63 K. This suggests that the experimental data at 59 K might be attributed to other factors, other than confinement effects. An imperfect surface is suggested and, employing 5% defects on this surface, the 2D critical temperature has been determined as 58 K which is in better agreement with the experimental value of 59 K.

Quantifying Pathways and Friction of Nanoparticles During Controlled Manipulation by Contact-Mode Atomic Force Microscopy

Measuring interfacial friction during the manipulation of nanoparticles is becoming an increasingly important approach in nanotribology research. In this work, antimony and gold particles deposited on flat graphite surfaces have been translated by the tip of an atomic force microscope in contact mode along defined pathways. Two different manipulation techniques are discussed with respect to pathway control and friction quantification. The first technique includes pushing the particles from the side, which often results in a loss of the particle during translation due to unwanted sidewards motion. We analyze this phenomenon with an analytical model and find good agreement with experiments. An alternative approach is to move the particle while the tip remains on its top. We demonstrate that this approach allows better manipulation pathway control and that simultaneous interfacial friction measurements are in quantitative agreement with the first manipulation method.

On the Strength of the Hydrogen−Carbon Interaction as Deduced from Physisorption

We deduce a new value for the potential well depth for the C-H2 interaction on the basis of experimental validations of isotherms of H2 and D2 predicted using independently characterized microstructural parameters. We use two carbons, one an activated carbon fiber whose structure has been recently characterized by us (Nguyen, T. X.; cohaut, N.; Bae, J.-S.; Bhatia, S. K. Langmuir 2008, 24, 7912) using hybrid reverse Monte Carlo simulation (HRMC) and the other the commercial Takeda 3A carbon molecular sieve whose pore size distribution is determined here from the 273 K CO2 adsorption isotherm. The conventional grand canonical Monte Carlo simulation technique incorporating a semiclassical Feynman and Hibbs (FH) potential approximation (FHGCMC) as well as path integral Monte Carlo calculations is employed to determine theoretical adsorption isotherms. It is found that curvature enhances the well depth for the LJ C-H2 interaction by a factor of 1.134 over that for a flat graphite surface, consistent with our recent study (Nguyen, T. X.; cohaut, N.; Bae, J.-S.; Bhatia, S. K. Langmuir 2008, 24, 7912). A value of the C-C well depth of 37.26 K, used for estimating the C-H2 well depth in conjunction with the Berthelot rules, with the Steele C-C well depth used for interaction with heavier gases (Ar, CO2 and CH4), leads to excellent agreement with experimental isotherms in all cases.