Low Coverage Regime Research Articles

Quantitation of IgG protein adsorption to gold nanoparticles using particle size measurement

The attachment of proteins, and other biomolecules, to nanoparticles is of critical interest both in the development of medical products using nanoparticles and in understanding the behaviour and fate of nanoparticles in biological systems. Measuring the amount of protein attached to the particles is a fundamental step in these regards and there are a variety of methods available for this purpose. In this work, we compare the use of three methods which measure particle diameter: Dynamic Light Scattering (DLS), Nanoparticle Tracking Analysis (NTA) and Differential Centrifugal Sedimentation (DCS). The choice of gold particles also permits measurement of the amount of adsorbed protein through a shift in plasmon frequency in UV-visible spectroscopy. When the protein layer is complete, the results from all methods are consistent to within ∼20% scatter and suggest that IgG adsorption on these 20 nm to 80 nm nanoparticles is rather similar to adsorption on flat gold surfaces with a water content of ∼60% by volume. We note an excellent correlation between plasmon frequency shift and DCS sedimentation times which indicates that both DCS and analytical ultracentrifugation can provide precise measurement of the thickness of complete protein shells on dense nanoparticles, but also show that these methods will fail for particles with a density of ∼1.38 g cm−3. In the low protein coverage regime, the measured amount of protein depends upon the technique: NTA and DLS provide, as expected, similar values that also correlate well with plasmon frequency shift. DCS analysis underestimates protein shell thicknesses in this regime and this may be explained through redistribution of the protein shell which reduces the frictional force during sedimentation. Crown copyright ©2013. Reproduced with the permission of the controller of HMSO.

The Chemistry of Water on α-Alumina: Kinetics and Nuclear Quantum Effects from First Principles

Water adsorption on an alumina (α-Al2O3) surface is studied here from first principles using periodic density functional theory in the generalized gradient approximation. Two different coverage regimes, low and high, are considered. For the low-coverage regime (with a coverage of 1/4 with respect to the number of coordinatively unsaturated Al sites), possible reactions at the surface such as dissociation, rotation, and diffusion of water and its fragments are investigated, using first principles thermodynamics and kinetics. A microkinetic model is set up with rates calculated from Eyring’s transition state theory in order to cover a wide range of time scales. Special emphasis of this study is on the magnitude of quantum effects and on anharmonic corrections, particularly for reactions and dynamics. These have often been neglected in the past for water/alumina systems but can influence the system. This is particularly true for processes involving hydrogen atoms, where, for example, tunneling corrections to reaction rates are found to be important even at room temperature. For a higher-coverage regime (with a coverage of 2 ML), hydrogen dynamics becomes even more complex and is characterized, e.g., by concerted atom motion, strong anharmonicity, and delocalization. In this regime, classical molecular dynamics becomes questionable as well as quantum mechanical treatments based on the harmonic approximation.

Structural study of monolayer cobalt phthalocyanine adsorbed on graphite

We present microscopic investigations on the two-dimensional arrangement of cobalt phthalocyanine molecules on a graphite (HOPG) substrate in the low coverage regime. The initial growth and ordering of molecular layers is revealed in high resolution scanning tunneling microscopy (STM). On low coverages single molecules orient mostly along one of the substrate lattice directions, while they form chains at slightly higher coverage. Structures with two different unit cells can be found from the first monolayer on. A theoretical model based on potential energy calculations is presented, which relates the two phases to the driving ordering forces.

Binding Geometry of Hydrogen-Bonded Chain Motif in Self-Assembled Gratings and Layers on Ag(111)

Upon adsorption on the (111) facet of Ag, 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA) self-assembles into a highly ordered, chiral twin chain structure at submonolayer coverages with domains that can extend for micrometers in one dimension. Using polarization-dependent measurements of C and N K-shell excitations in near-edge X-ray absorption fine structure (NEXAFS) spectra, we determine the binding geometry of single PVBA molecules within this unique ensemble for both low and high coverage regimes. At submonolayer coverage, the molecule is twisted to facilitate the formation of hydrogen bonds. The gas-phase planarity is gradually recovered as the coverage is increased, with complete planarity coinciding with loss of order in the overlayer. Thermal treatment of the PVBA film results in deprotonation of the carboxyl tail of the molecule, but despite the suppression of the stabilizing hydrogen-bonds, the overlayer remains ordered.

Atomic-scale study of the adsorption of calcium fluoride on Si(100) at low-coverage regime

We investigate, experimentally and theoretically, the initial stage of the formation of Ca/Si and Si/F structures that occurs during the adsorption of CaF${}_{2}$ molecules onto a bare Si(100) surface heated to 1000 K in a low-coverage regime (0.3 monolayer). A low-temperature (5 K) scanning tunneling microscope (STM) is used to observe the topographies and the electronic properties of the exposed silicon surfaces. Our atomic-scale study reveals that several chemical reactions arise during CaF${}_{2}$ deposition, such as dissociation of the CaF${}_{2}$ molecules and etching of the surface silicon dimers. The experimental and calculated STM topographies are compared using the density functional theory, and this comparison enables us to identify two types of reacted structures on the Si(100) surface. The first type of observed complex surface structure consists of large islands formed with a semiperiodic sequence of 3 \ifmmode\times\else\texttimes\fi{} 2 unit cells. The second one is made of isolated Ca adatoms adsorbed at specific sites on the Si(100)-2 \ifmmode\times\else\texttimes\fi{} 1 surface.

Terthiophene on Au(111): A scanning tunneling microscopy and spectroscopy study

Terthiophene (3T) molecules adsorbed on herringbone (HB) reconstructed Au(111) surfaces in the low coverage regime were investigated by means of low-temperature scanning tunneling microscopy (STM) and spectroscopy (STS) under ultra-high vacuum conditions. The 3T molecules adsorb preferentially in fcc regions of the HB reconstruction with their longer axis oriented perpendicular to the soliton walls of the HB and at maximum mutual separation. The latter observation points to a repulsive interaction between molecules probably due to parallel electrical dipoles formed during adsorption. Constant-separation (I-V) and constant-current (z-V) STS clearly reveal the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals, which are found at −1.2 eV and +2.3 eV, respectively. The HOMO–LUMO gap corresponds to that of a free molecule, indicating a rather weak interaction between 3T and Au(111). According to conductivity maps, the HOMO and LUMO are inhomogeneously distributed over the adsorbed 3T, with the HOMO being located at the ends of the linear molecule, and the LUMO symmetrically with respect to the longer axis of the molecule at the center of its flanks. Analysis of spectroscopic data reveals details of the contrast mechanism of 3T/Au(111) in STM. For that, the Shockley-like surface state of Au(111) plays an essential role and appears shifted outwards from the surface in the presence of the molecule. As a consequence, the molecule can be imaged even at a tunneling bias within its HOMO–LUMO gap. A more quantitative analysis of this detail resolves a previous discrepancy between the fairly small apparent STM height of 3T molecules (1.4–2.0 nm, depending on tunneling bias) and a corresponding larger value of 3.5 nm based on X-ray standing wave analysis. An additionally observed linear decrease of the differential tunneling barrier at positive bias when determined on top of a 3T molecule is compared to the bias independent barrier obtained on bare Au(111) surfaces. This striking difference of the barrier behavior with and without adsorbed molecules is interpreted as indicating an adsorption-induced dimensionality transition of the involved tunneling processes.

Theoretical study on the sequential hydroxylation of C82 fullerene based on Fukui function

In the present work semi-empirical PM3 method and ab initio density-functional theory calculations were performed in carbon systems. The condensed Fukui function was calculated and HOMO–LUMO were visualised in order to study the sequence of hydroxylation of two isomers of C82 fullerene for the low coverage regime, with the formula C82(OH) x where x = 0 − 12. It was found that there was a formation of dangling bonds on structures with an odd number of hydroxyl groups on the fullerene surface, which suggests an enhanced reactivity of these molecules. Nevertheless, the coverings with an even number of groups tend to the reconstruction of π bonds, obtaining less reactive molecular structures. With the adsorption of the first group, a narrow HOMO–LUMO gap (1.28 eV) is observed in comparison with the C82(OH)2 system (1.70 eV), as is found in similar systems, such as C60 fullerenol [E.E. Fileti et al., Nanotechnology 19, 365703 (2008); J.G. Rodríguez-Zavala and R.A. Guirado-López, Phys. Rev. B 69, 075411 (2004)]. Through an analysis of the electronic structure to these coverings, a splitting of electronic energy levels in the structure with one hydroxyl group is observed, which could be one of the factors that causes the narrowing of the energy gap in this structure. On the other hand, with a coverage of 12 hydroxyl groups, the formation of an amphiphilic molecule, where the location of groups in one side of the C82 surface provides an hydrophilic character, is observed, while the uncovered part has an hydrophobic character. This could be important in the formation of Langmuir monolayers. Finally, it is shown that the precise distribution of the OH groups on the fullerene surface plays a crucial role in the electronic structure of the polyhydroxylated fullerenes.

Electron transfer reaction through an adsorbed layer

Electron transfer from a redox to an electrode through an adsorbed intermediate is considered in this paper. The formalism is developed to cover all regimes of coverage factor, from lone adsorbate to monolayer regime. The randomness in the distribution of adsorbates is handled using coherent potential approximation. Current–overpotential profile for all coverage regime is provided. Explicit analysis of the low and high coverage regime is done by supplementing with the density of states ( dos) profile for adsorbate in both weak and strongly coupled sectors. The prominence of bonding and anti-bonding states in the strongly coupled adsorbates at low coverage gives rise to saddle point behaviour in the current–overpotential profile. The variation of current with overpotential at low coverage is consistent with the Marcus inverted region prediction and the traditional direct electron transfer behaviour at high coverage is recovered through the present analysis.

Coverage and charge dependent adsorption of butanethiol on the Au(1 1 1) surface: A density functional theory study

A theoretical study based on periodic DFT calculations of the structure, the surface bonding, and the energetics of butanethiols adsorbed on the Au(1 1 1) surface is reported. Several sites and coverage have been considered, and neutral and charged metal surfaces have been simulated. Whatever the coverage is, the preferred site is a hollow-bridge type-site in which sulfur atom simultaneously binds to two gold atoms. Thiol adsorption parameters are sensitive to the coverage, especially the adsorption energy that shows a clear response to the number of thiols adsorbed, and the thiol-surface interaction decreases when the coverage grows as the lateral repulsion between the alkyl tails weaken the strength of the Au-S bond. The thiol-surface interaction parameters are also sensitive to the charge of the metal. Also, we found that the adsorption becomes more favorable when the metal surface is negatively charged, and less favorable on positive surfaces. Finally, in order to analyze dynamical effects, we performed a molecular dynamics (MD) simulation considering a system with ethanethiol on an Au slab pre-covered by water. The MD simulation shows that the proton transfer occurs within a few femtoseconds and that prior to the transfer itself, the sulfur atom binds to a gold surface atom. This Au atom is clearly pulled out of the surface, what could be interpreted as the onset of the islands and cluster formation already observed in the low coverage regime.

A Simulation Study of Hydrogen in Metal–Organic Frameworks

Molecular simulations have been used to evaluate the effect exerted by metal centres on the adsorption and diffusion of hydrogen in metal-organic frameworks. Simulations were carried out for the MIL-53 (Cr and Al) structures and the isostructural vanadium analogue MIL-47 at room temperature. To validate the models and force fields used in this work, the adsorption isotherms, energies and entropies, and self-diffusivities in Cu-BTC and IRMOF-1 metal-organic frameworks were computed. Using the validated force fields and models, a detailed analysis of the preferential adsorption sites is reported, allowing the energetic contribution in the low-coverage regime (Henry constants and adsorption energies and entropies) to be determined as a function of loading (adsorption isotherms). The influence of each energetic contribution to the charged and uncharged models of hydrogen has also been analyzed.

The adsorption of a substituted benzene, the ethynyl-trifluoro-toluene on Si(100)-2 × 1

The adsorption of 3-ethynyl-trifluoro-toluene (ETFT) on Si(100)-2 × 1 surface in ultra high vacuum is studied in the low coverage regime, through a joint experimental and theoretical approach. The STM images of both filled and empty states revealed few distinct adsorption configurations. On the basis of Density Functional Theory (DFT) calculations the STM images were simulated and three main adsorption configurations were identified, with a predominance of di-sigma bonded species that leave the benzene ring unreacted. A discussion of the reactivity of the reconstructed silicon surface towards benzene derivatives is proposed by comparing the adsorption of ETFT close related molecules, like styrene and phenylacetylene.

Cobalt oxide nanolayers on Pd(100): The thickness-dependent structural evolution

The growth of interface-stabilized cobalt oxide (CoO x) nanolayers on Pd(100) has been investigated and their structures are reported as a function of coverage. Several different phases have been observed by LEED and STM experiments, and they have been characterized spectroscopically by photoemission and X-ray absorption. The data indicate that in the low coverage regime (up to Θ Co ≈ 2–3 ML) rock-salt CoO type phases are formed (defective in the single layer regime, and stoichiometric in multilayers) with (100) or (111) termination. At higher coverage (Θ Co ≈ 10–20 ML) spinel Co 3O 4(111) and CoO(100) layers have been detected, in ratios dependent on the preparation conditions. The observed structures are discussed in relation to similar structures reported recently for CoO x films on Ir(100) [W. Meyer et al., J. Phys.: Condens. Matter 20 (2008) 265011].

Asymmetric relief of surface stress induced by a chiral adsorbate: Alaninate adsorption on Cu(110)

Using first-principles calculations, we explore symmetry breaking in the surface stress tensor induced upon adsorption of chiral species on an achiral metallic substrate, namely, alaninate on Cu(110). The stress sensitivity to coverage and adsorption geometry is studied in the known $(2\ifmmode\times\else\texttimes\fi{}3)$ phase and other related reconstructions. We find that alaninate relieves stress in the Cu(110) surface by electron transfer from the substrate to the molecule. In a low coverage regime, $\ensuremath{\Theta}=1/6$, the principal stresses are found to deviate in opposite directions by an angle $\ensuremath{\alpha}\ensuremath{\sim}15\ifmmode^\circ\else\textdegree\fi{}$ from the substrate mirror plane directions, $[1\overline{1}0]$, depending on the chirality of the alaninate adsorption footprint. In medium-high coverage regimes, $\ensuremath{\Theta}\ensuremath{\ge}0.3$, the observed asymmetries are weaker, consistent with the presence of H bonds lying close to $[1\overline{1}0]$. The studied $\ensuremath{\Theta}=1/3$ enantiopure models show the same asymmetry orientation with $\ensuremath{\alpha}\ensuremath{\sim}5\ifmmode^\circ\else\textdegree\fi{}$. Thus, stress relief anisotropy is diagnostic of the molecular chirality in this case. We also find that the substrate intrinsic tensile stress is relieved at $\ensuremath{\Theta}\ensuremath{\gtrsim}0.25$, when the adsorbates form the onset of a H-bound network. At higher coverages, the system is under net compressive stress.

Surface Reaction of Sulfur-Containing Amino Acids on Cu(110)

Adsorption behaviors of sulfur-containing amino acids, cysteine, methionine, and cystine molecules on Cu(110) surface were studied by core level photoelectron spectroscopy using synchrotron radiation. We found the following through the systematic comparisons of core level peaks such as S 2p, N 1s, and O 1s from different amino acids. At low coverage regimes, all the molecules form two distinct thiolate species, and their S 2p binding energy difference was about 0.9 eV. The relative populations of the two thiolates were different for different molecules and their coverage, which is due to the different bond strength of the sulfur-containing functional groups. At high coverage regimes, only cysteine molecules form zwitterionic state, which is related to the molecular ordering on Cu(110) surface.

Au(111)-Based Nanotemplates by Gd Alloying

A new class of nanostructured templates is obtained by submitting Au111 films to high-temperature vapor deposition of Gd in ultrahigh vacuum. In a low coverage regime, Gd atoms are embedded in the topmost Au layer, inducing a structural transformation of the herringbone reconstruction to create a network of trigons. At higher dose, the reactive deposition of Gd leads to the formation of an atomically perfect GdAu2 surface compound characterized by a long-range periodic Moire pattern. Both the trigon and Moire lattices are highly ordered nanostructures, which turned out to be robust templates to grow metal nanodots. As a test example, Co was deposited at room temperature, forming uniform dots that faithfully arrange by following the underlying trigons or Moire periodicity. For the latter, one can achieve nanodot arrays that exhibit record areal density.

Atomic structure of the (3 × 2) Si–GaAs (0 0 1) reconstructed surface: A clue to δ doping mechanism derived from in situ grazing incidence X-ray diffraction data

In view of understanding silicon incorporation in the δ doping process of GaAs (0 0 1), Si atoms have been deposited, under UHV, on a α(2 × 4) arsenic terminated substrate. In the low coverage regime, a transition to a less As rich (3 × 2) reconstructed Si–GaAs (0 0 1) surface was observed whose atomic structure has been investigated by grazing incidence X-ray diffraction performed in situ. Silicon is found to occupy not only a Ga substitutional site, precursor of a donor dopant but also to form nuclei for neutral clusters, on a template made by the (3 × 2) GaAs (0 0 1) reconstructed surface observed by Martrou et al. [Phys. Rev. B 72 (2005) 241307®]. The maximum surface concentration of donor-like silicon is estimated at 1.04 × 10 14 cm −2 (1/6th monolayer).

Barium adsorption on the chemisorbedO(2 × 1)/Ni(110) surface

Barium adsorption on the O(2 × 1)/Ni(110) surface has been studied by Auger electron spectroscopy and work function measurementsin combination with photoemission measurements. The study was focused on the lowcoverage regime from submonolayer to double monolayer. The results show that duringdevelopment of the first layer of Ba on the surface, a two-dimensional incompletebarium oxide layer, BaO, forms. This BaO layer is interspersed by Ba chemisorbedatoms reacting directly with Ni atoms. As the second layer of Ba is completed, theadsorbate approaches the metallic phase due to the Ba–Ba interaction. The lowenergy Auger transition lines of Ba (75 eV) and BaO (68 eV) shift towards lowerenergies as the Ba coverage increases. Previous photoemission measurements bysynchrotron radiation are used to interpret these energy shifts, which are closelyrelated to the barium oxidation process on the surface. The analysis shows theimportance of the extra-atomic relaxation energy due to (1) the polarization of theO2− anions from BaO and (2) the screening from the electron density at the Fermi level of thebarium overlayer and the nickel substrate.

Energetics of oxygen adsorption and incorporation at InN polar surface: A first‐principles study

AbstractFirst principles calculations are performed to study the adsorption and incorporation of oxygen at InN polar surfaces as a function of oxygen coverage. We find that the adsorption of oxygen at InN surfaces is higher on the N‐polar than on In‐polar. The calculations show that for the low coverage regime (x ≤ 0.5 ML) both orientations are active towards the adsorption of oxygen; this implies that the reaction between the O atoms and the surface is strongly exothermic. As the coverage of O exceeds 0.5 ML a large difference in adsorption energies, of almost 2.5 eV, is observed between (0001) and (000$ \bar 1 $) surfaces indicating that the (000$ \bar 1 $) surface is more active towards oxygen adsorption than the (0001) surface. The high coverage of oxygen changes the surface structure of InN due to the difference in binding energy (O‐In bonds are stronger than In‐N ones). This result shows explicitly that the formation of In adlayer is disturbed by the O adsorption. Concerning the energetics of O incorporation our results show that it is more favourable for O to substitute a N atom in one of the top layers near the surface than in bulk, indicating that there is a strong tendency for O to reside at the surface rather than in subsurface layers. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Early stages of vanadium deposition on Si(1 1 1)-7 × 7

We investigate the low-coverage regime of vanadium deposition on the Si(1 1 1)-7 × 7 surface using a combination of scanning tunnelling microscopy (STM) and density-functional theory (DFT) adsorption energy calculations. We theoretically identify the most stable structures in this system: (i) substitutional vanadium atoms at silicon adatom positions; (ii) interstitial vanadium atoms between silicon adatoms and rest atoms; and (iii) interstitial vanadium – silicon adatom vacancy complexes. STM images reveal two simple vanadium-related features near the Si adatom positions: bright spots at both polarities (BB) and dark spots for empty and bright spots for filled states (DB). We relate the BB spots to the interstitial structures and the DB spots to substitutional structures.

CO2 + CH4 Chemistry over Pd: Results of Kinetic Simulations Relevant to Environmental Issues

We have determined the Arrhenius rate constants for 99 chemical reactions on palladium and solved the tightly coupled differential equations describing the chemical kinetics at a number of temperatures ranging from 350 to 700 K. The rate equations were integrated to a week of reactor run time. In this work, we discuss the valuable insights that can be gained by closely examining the chemistry ongoing on the first differential slice of the plug flow reactor. The two-component feed gas consisted of CO2 and CH4 with a total pressure of 1 bar. The CO2−CH4 partial pressures employed ranged from 20−80% to 80−20%. In these temperature and pressure ranges, the system performs in the low-coverage regime. In addition to the feed gas, formaldehyde, methanol, molecular hydrogen, C2 hydrocarbons, formic acid, acetic acid, ketene, water, and carbon monoxide evolve from the catalyst surface in the first differential slice of the plug flow reactor. The relative amounts of the desorbing reaction products are dependent on ...