The adsorption of adenine on mineral surfaces: Iron pyrite and silicon dioxide

The adsorption of the nucleobase adenine on surfaces of the minerals iron pyrite and silica has been studied by photoemission and soft X-ray photoabsorption spectroscopy. Pyrite samples were prepared by fracture under nitrogen followed by transfer to ultrahigh vacuum, or by cleavage in vacuum. By comparing data with multilayer spectra, adenine was found to chemisorb on pyrite, with small changes in the valence band spectrum, and stronger changes in the NEXAFS spectrum. The molecules were bonded with the molecular plane at a steep angle to the surface plane. On silica the molecule was found to adsorb at a reduced angle to the surface. The C and N 1s photoemission spectra on this surface suggest chemisorption, although the nitrogen NEXAFS spectra are similar to multilayer spectra.     

Ca掺杂的氧化铍纳米管吸附H2O和NH3的选择传感特

通过密度泛函计算, 借助NH₃和H₂O分子对未掺杂以及钙掺杂的BeO碳纳米管的结构和电传导性进行了研究. 结果发现,NH₃和H₂O分子可以吸附在纳米管侧壁的Be原子上,吸附能分别为约36.1和39.0 kcal/mol. 态密度分析显示BeO纳米管的电传导性在吸附后稍有变化. 对于NH₃和H₂O分子,纳米管表面的钙原子替换Be原子可使吸附能分别增加约7.4和14.7 kcal/mol. 与未掺杂纳米管不同的是,钙掺杂BeONT吸附NH₃和H₂O分子的电传导性更加敏感,且H₂O分子比NH₃分子更敏感.     

Interaction between fullerene-wheeled nanocar and gold substrate: A DFT study

Since the successful synthesis of nanocar and its surprising movement on the gold surface, several theoretical investigations have been devoted to explain the interaction properties as well as its movement mechanism on the substrate. All of them failed, however, to gain a clear theoretical insight into the respected challenges because of the weak computational methods implemented for this complex system including heavy metal atoms and giant size of the whole system. In this work, we have investigated the adsorption of fullerene-wheeled nanocar onto a Au (1 1 1) substrate using the comprehensive first-principles density functional theory (DFT) simulations. The binding energy between the nanocar and Au (1 1 1) surface was determined to be −9.43 eV (−217.45 kcal/mol). The net charge transfer from the nanocar to the gold substrate was calculated to be about 9.56 electrons. Furthermore, the equilibrium distances between the Au surface and the C₆₀ molecule and nanocar chassis were estimated to be 2.20 Å and 2.30 Å, respectively. The BSSE correction was also considered in the binding energy estimation and the result show that the BSSE correction significantly affects the calculated binding energy for such systems.Finally, we have performed ab initio molecular dynamics simulation for a single C₆₀ fullerene on the gold surface at room temperature. Our first-principles result shows that ambient condition affect remarkably on the adsorption property of fullerene on the gold surface. We also observed that the C₆₀ fullerene wheel slips by approximately 3.90 Å within 5 ps of simulation time at 300 K.     

Arsenic pentafluoride surface adsorption studies on Kagome-phosphorene – a DFT outlook

Arsenic pentafluoride (AsF₅) is a highly toxic gas molecule that finds its application in the manufacturing of electro-conductive polymers. Besides, exposure to AsF₅ molecule may invite several health issues, for instance, central-nervous-system disorders. Thus, the detection of AsF₅ gas is a significant and important concern for public health. For the very first time, we built a novel Kagome phosphorene nanosheet (Kagome-PNS) to study the adsorption behavior of AsF₅ molecule on the Kagome-PNS surface using density-functional theory method. The Kagome-PNS owns semiconductor property with an energy gap value of 1.22 eV. Initially, the geometrical stability of Kagome-PNS was verified with the negative value of cohesive formation energy. The transport properties of Kagome-PNS have also been carried out using current-voltage characteristics. Moreover, AsF₅ gas molecules are physisorbed on Kagome-PNS, the adsorption energy of the preferential complex structures is found to be −0.099 to −0.377 eV. An innovative finding of the present study acclaims that Kagome-PNS can be proficiently used as a chemical sensor to detect AsF₅ gas molecules.     

F−, Cl−, Li+ and Na+ adsorption on AlN nanotube surface: A DFT study

Adsorption of two anions (F⁻ and Cl⁻) and two cations (Li⁺ and Na⁺) on the surface of aluminum nitride nanotubes (AlNNTs) is investigated by density functional theory. The reactions are site-selective, so that the cations and anions prefer to be adsorbed atop the N and Al atoms of the tube surface, respectively. The adsorption energies of anions (−4.46 eV for F⁻ and −1.12 eV for Cl⁻) are much higher than those of cations (about −0.17 eV for Li⁺ and −0.12 eV for Na⁺) which can be explained using frontier molecular orbital theory. It was found that the adsorption of anions may facilitate the electron emission from the AlNNT surface by reducing the work function due to the charge transfer occurs from the anions to the tube. It has been predicted that in contrast to the cations the adsorption of anions also obviously increases the electrical conductivity of AlNNT.     

Sodium affinity of caffeine and adenine: the effect of microsolvation and electrostatic field of solvent on the sodium affinity

The sodium affinity (SA) of caffeine (CAF), adenine (AD) and their microsolvated clusters containing one X molecule (CAF-X and AD-X; X = H₂O, NH₃, H₂S and HF) has been calculated in the gas phase and water, separately. The density functional theory (DFT) employing CAM-B3LYP functional has been used for all of the calculations in this work. The solvent was modelled by the polarised continuum model (PCM) which considers the electrostatic field of solvent on solute. The calculated SA of [CAF-X] and [AD-X] was higher than that of CAF and AD in the gas phase, respectively, which showed that the microsolvation of molecules in the gas phase could be used for changing the tendency of molecules for binding to Na⁺. Also, it was observed that the electrostatic effect of solvent decreases the SA of the species compared to the gas phase, considerably. The symmetry adapted perturbation theory (SAPT) calculations were also used to interpret the change in the SA of CAF and AD due to the clustering with one X molecule in the gas phase. In addition, there is a detailed study on the position of Na⁺ relative to AD and CAF structures in different conditions including gas phase, microsolvation and electrostatic field of solvent in this work.     

Hybrid HF–DFT modeling of monolayer water adsorption on (001) surface of cubic BaHfO3 and BaZrO3 crystals

First-principles calculations have been used to study the atomic structure, preferred sites and adsorption energies for water adsorption at different terminations of the cubic phase of perovskite-structured BaHfO₃ and BaZrO₃. By considering different initial positions of water molecules, the possibility of water dissociation has been investigated. It is demonstrated that the site selectivity and the form of adsorbed molecule can be affected by the choice of surface unit cell. Dissociative adsorption was found to be favorable for all surfaces in consideration. Hydroxylation of ZrO₂- and HfO₂-terminated surfaces is accomplished by a noticeable reconstruction of the surface structure of cubic phase towards the orthorhombic phase. Calculated atomic charges in bare and hydroxylated surfaces show that BaHfO₃ crystal is slightly more ionic than BaZrO₃.     

Theoretical study on adsorption of Au and hydrated Au cations on clean Si(1 1 1) surface

To model the adsorption of Au⁺ cation in aqueous solution on the semiconductor surface, the interactions of Au⁺ and hydrated Au⁺ cations with clean Si(1 1 1) surface were investigated by using hybrid density functional theory (B3LYP) and Møller-Plesset second-order perturbation (MP2) methods. Si(1 1 1) surface was described with Si₇H₁₁, Si₁₁H₁₇ and Si₂₂H₂₁ clusters. The effect of the basis set superposition error (BSSE) was taken into account by applying the counterpoise correction. The calculated results indicated that the binding energies between hydrated Au⁺ cations and clean Si(1 1 1) surface are large, suggesting a strong interaction between hydrated Au⁺ cations and the semiconductor surface. The bonding nature of the chemical adsorption of Au⁺ to Si surface can be classified as partial covalent as well as ionic bonding. As the number of water molecules increases, the water molecules form hydrogen bond network with one another and only one water molecule binds directly to the Au⁺ cation. The Au⁺ cation in aqueous solution will safely attach to the clean Si(1 1 1) surface.     

Rotational parity and separation of water molecules into spin isomers

A theoretical explanation is proposed for the effect of variations in concentration of water molecule spin isomers in the gas phase during the interaction of molecules with a solid adsorbent surface. The explanation is based on antisymmetric (AS) correlation between proton spin moments and molecule rotation. A new AS correlation occurs during the interaction of the molecule with a dc electric field near the surface. Due to the new (external) AS correlation, ortho-and parawater molecules are formed; separation into spin modifications occurs over degenerate states of each rotational level of the molecule. Water molecule separation into spin modifications at the previous (internal) AS correlation occurs over rotational levels of molecules. The ratio of ortho-and parawater concentrations in the gas phase at the external AS correlation is compared with experimental data on chromatographic separation of water spin isomers. Quantitative agreement is observed between the calculated ratio and the ratio measured for water molecules at the final separation stage.     

Theoretical insight of adsorption thermodynamics of multifunctional molecules on metal surfaces

Adsorption thermodynamics based on density functional theory (DFT) calculations are exposed for the interaction of several multifunctional molecules with Pt and Au(1 1 0)-(1 × 2) surfaces. The Gibbs free adsorption energy explicitly depends on the adsorption internal energy, which is derived from DFT adsorption energy, and the vibrational entropy change during the chemisorption process. Zero-point energy (ZPE) corrections have been systematically applied to the adsorption energy. Moreover the vibrational entropy change has been computed on the basis of DFT harmonic frequencies (gas and adsorbed phases, clean surfaces), which have been extended to all the adsorbate vibrations and the metallic surface phonons. The phase diagrams plotted in realistic conditions of temperature (from 100 to 400 K) and pressure (0.15 atm) show that the ZPE corrected adsorption energy is the main contribution. When strong chemisorption is considered on the Pt surface, the multifunctional molecules are adsorbed on the surface in the considered temperature range. In contrast for weak chemisorption on the Au surface, the thermodynamic results should be held cautiously. The systematic errors of the model (choice of the functional, configurational entropy and vibrational entropy) make difficult the prediction of the adsorption-desorption phase boundaries.     

Adsorption of water molecule on (001) and (110) surfaces of MgH2

First principle calculations have been performed to explore the adsorption characteristics of water molecule on (001) and (110) surfaces of magnesium hydride. The stable adsorption configurations of water molecule on the surfaces of MgH₂ were identified by comparing the total energies of different adsorption states. The (110) surface shows a higher reactivity with H₂O molecule owing to the larger adsorption energy than the (001) surface, and the adsorption mechanisms of water molecule on the two surfaces were clarified from electronic structures. For both (001) and (110) surface adsorptions, the O p orbitals overlapped with the Mg s and p orbitals leading to interactions between O and Mg atoms and weakening the O–H bonds in water molecule. Due to the difference of the bonding strength between O and Mg atoms in the (001) and (110) surfaces, the adsorption energies and configurations of water molecule on the two surfaces are significantly different.     

DFT calculations of adenine adsorption on coin metal (1 1 0) surfaces

Density functional theory is used to analyze in detail the adsorption of the adenine molecule on the (1 1 0) surfaces of Cu, Ag, and Au. While the adsorption configurations are similar in all three cases – the molecule bonds via two nitrogen atoms to the substrate – the details like charge transfer or local strain a rather different. The molecule–substrate interaction in case of Cu is stronger than for the more noble metals Ag and Au. Longe-range dispersion forces stabilize the adsorption configuration in dependence on the specific adsorption geometry. In case of Ag and Au, relativistic effects are found to be important.     

Adsorption of glycine on diamond(001): Role of bond angle of carbon atoms

The adsorption behaviors of glycine on diamond(001) are systematically investigated by first-principles calculations.We have considered all possible adsorption configurations without a surface dangling bond and give a quantitative analysis for the relationship between the deviation of carbon bond angle and adsorption energy. We found that a smaller distortion of carbon covalent bond angle results in a more stable adsorption structure, and the most stable adsorption has a benzene-ringlike structure with the highest adsorption energy of 5.11 e V per molecule and the minimum distortion of carbon covalent bond angle.     

AlGaN barrier thickness dependent surface and interface trapping characteristics of AlGaN/GaN heterostructure

The aluminium gallium nitride (AlGaN) barrier thickness dependent trapping characteristic of AlGaN/GaN heterostructure is investigated in detail by frequency dependent conductance measurements. The conductance measurementsin the depletion region biases (−4.8 V to −3.2 V) shows that the Al_0.3Ga_0.7N(18 nm)/GaN structure suffers from both the surface (the metal/AlGaN interface of the gate region) and interface (the AlGaN/GaN interface of the channel region) trapping states, whereas the AlGaN/GaN structure with a thicker AlGaN barrier (25 nm) layer suffers from only interface (the channel region of AlGaN/GaN) trap energy states in the bias region (−6 V to −4.2). The two extracted time constants of the trap levels are (2.6–4.59) μs (surface) and (113.4–33.8) μs (interface) for the Al_0.3Ga_0.7N(18 nm)/GaN structure in the depletion region of biases (−4.8 V to −3.2 V), whereas the Al_0.3Ga_0.7N (25 nm)/GaN structure yields only interface trap states with time constants of (86.8–33.3) μs in the voltage bias range of −6.0 V to −4.2 V. The extracted surface trapping time constants are found to be very muchless in the Al_0.3Ga_0.7N(18 nm)/GaN heterostructure compared to that of the interface trap states. The higher electric field formation across the AlGaN barrier causes de-trapping of the surface trapped electron through a tunnelling process for the Al_0.3Ga_0.7N(18 nm)/GaN structure, and hence the time constants of the surface trap are less.     

Kinetics of water molecule adsorption on the porous silicon surface

The kinetics of water vapor adsorption on the porous silicon surface is studied by the gas relaxometry method. The process multistepping which is reflected in sequential changes in H₂O molecule diffusivities into the porous matrix, is found. Phenomenological models describing the experiment are considered.     

Desorption of carbon dioxide from small potassium niobate particles induced by the particles’ ferroelectric transition

The aim of this work is to understand surface properties of ferroelectric crystals related to gas adsorption. Various ferroelectric crystals involved in these studies readily adsorb carbon dioxide, thus our studies were centered on adsorption studies of this molecule. It has been claimed that a dipole moment is induced on carbon dioxide molecules that are near an oxide surface. Our experiments explored the possibility of a dipole-dipole interaction between the gas molecule and the ferroelectric oxide surface in order to explain its adsorption. We characterized the samples with scanning electron microscopy, X-ray diffraction and Raman spectroscopy. We determined the ferroelectric nature of the particles and studied the temperature-dependent phase transitions in small particles of KNbO₃ using Raman spectroscopy. We were able to correlate desorption of CO₂ from one surface state of KNbO₃ with the occurrence of the orthorhombic to tetragonal transition in KNbO₃ in particles of 1 μm size. This CO₂ surface site was not observed in KTaO₃, which does not show ferroelectricity at room temperature.     

Adsorption Properties of β‐Cyclodextrin for Adsorbing Aromatic Hydrocarbons from the Gas Phase and Water

β‐cyclodextrin (β‐CD) is a potentially useful adsorbent for the adsorption of aromatic hydrocarbons from the gas phase and water. In this paper, the adsorption properties of β‐CD for adsorbing six aromatic hydrocarbons from the gas phase and seven aromatic hydrocarbons from water were measured. The inverse gas chromatography (IGC) technique was used to characterize the Flory interaction parameters of β‐CD and the six aromatic hydrocarbons from the gas phase at 40, 50, 60, and 70°C. For these aromatic hydrocarbons, the order of β‐CD adsorption ability from strong to weak was: styrene>ethylbenzene>o‐xylene>chlorobenzene>toluene>benzene. For the seven aromatic hydrocarbons in water, adsorption values α, were measured at 20, 30, 40, and 50°C. The order of β‐CD adsorption ability from strong to weak was: ethylbenzene>o‐xylene>styrene>chlorobenzene>toluene>benzene>phenol. This trend was explained based on their solubility degrees in water. It was found that the adsorption abilities of β‐CD for adsorbing aromatic hydrocarbons from the gas phase and water have a similar trend.     

Equilibrium adsorption of water-like molecules on single nanospheres

Water-like gas adsorption on spherical nano-aerosol particles has been studied for particles of different sizes at different temperatures with density functional theory. The water-like fluid was modelled as Lennard–Jones (LJ) spheres with four hydrogen-bonding sites with parameters adjusted to the phase diagram of water. For the single sphere case, both the adsorption excesses and density profiles approach those of the plane cases as the spherical substrate sizes increase; at each temperature studied, the size dependence of the transition from thin-film adsorption to thick-film adsorption has been observed. What we found here support earlier suggestions (J. X. Fang, W. H. Marlow, J. X. Lu, and R. R. Lucchese, J. Chem. Phys. 107, 5212 (1997)) that not only the interaction energies between the water molecule and the spherical substrate are sensitive to the size of the spherical substrate, but also the wetting behaviour. In calculations of the excess adsorptions of particles of radii R?=?20σ, 30σ, and 50σ, these substrates show the expected transition from the single molecule to the macroscopic aerosol particles.     

XPS,UPS and thermal desorption studies of alcohol adsorption on Cu(110): II. Higher alcohols

Preceding work dealing with the adsorption of methanol on Cu(110) has been extended to include ethanol, n- and iso-propanol and a diol, ethylene glycol. In common with the simplest alcohol, all these molecules are able to form a stable alkoxy species on the surface, that is, the alcohol dissociated at the O-H group. However, in contrast to methanol on the clean surface for which the dissociated methoxy and hydrogen recombined to desorb as methanol, all the higher alcohols reacted further with the surface, dehydrogenating to yield the corresponding aldehyde or ketone in the gas phase. Ethylene glycol reacted to form the most strongly bound intermediate of all, decomposing near 390 K to produce the dialdehyde, glyoxal, with little evidence of monoaldehyde formation or C-C bond breakage. The influence of pre-adsorbed oxygen on these reactions was to generally increase the amount of alkoxy formed on the surface by enhancing the amount of dissociative adsorption (water is formed by the deprotonation of adsorbed alcohol molecules by oxygen atoms). The alkoxide decomposition peaks were shifted to slightly higher temperatures and considerably broadened in such experiments. The decomposition peak temperatures of the different surface alkoxides correlate fairly well with literature values of the αC-H bond strength, which is weaker in iso-propanol than in methanol. XPS showed broad O(1s) spectra for all the molecules adsorbed at 140 K, probably due to hydrogen-bonding effects in the adlayer, with peak emissions at around 533 eV. When the surface was warmed to 250 K, the O(1s) spectra narrowed to close to instrumental linewidths with a concomitant shift to a lower binding energy near 531 eV. C(1s) spectra showed little change between the adsorbed alcohol and alkoxy species. The UPS showed low temperature spectra similar to the gas phase, but the highest occupied orbitals, which are essentially O(2p) orbitals, showed a chemisorption bonding shift of several tenths of an electron volt. UPS for these molecules is shown to have considerable less utility than for the simplest molecule, methanol, due to the masking of possible orbital shifts during chemical changes on the surface by the presence of overlapping emissions in the spectra.     

Stimulation of vapor nucleation on perfect and imperfect hexagonal lattice surfaces

Monte Carlo simulations of water vapor nucleation on a perfect crystal surface and on a surface with defects are performed. Mass exchange with the vapor phase is modeled by using an open ensemble. Cluster-substrate interaction is described in terms of conventional atom-atom potentials. The Hamiltonian of the system includes expressions for electrostatic, polarization, exchange, and dispersion interactions. The Gibbs free energy and work of adsorption are calculated by Monte Carlo simulation in the bicano?nical ensemble. The microscopic structure of nuclei is analyzed in terms of pair correlation functions. Periodic boundary conditions are used to simulate an infinite substrate surface. Molecule-substrate and molecule-molecule long-range electrostatic interactions are calculated by summing the Fourier harmonics of the electrostatic potential. Dispersion interactions are calculated by direct summation over layers of unit cells. Nucleation on a surface with matching structure follows a layer-by-layer mechanism. The work of adsorption per molecule of a monolayer on the substrate surface has a maximum as a function of nucleus size. The steady rate of nucleation of islands of supercritical size is evaluated. The work of adsorption per molecule for layer-by-layer film growth is an oscillating function of cluster size. As a function of layer number, it has a minimum depending on the vapor pressure. The electric field generated by a microscopic surface protrusion destroys the layered structure of the condensate and eliminates free-energy nucleation barriers. However, point lattice defects do not stimulate explosive nucleation.