An augmented effective core potential basis set for the calculation of molecular polarizabilities

Calculations of molecular polarizabilities require basis sets capable of accurately describing the responses of the electrons to an external perturbation. Unfortunately, basis sets that yield suitable quantitative results have traditionally been all-electron sets with large numbers of primitives, making their use computationally intractable even for moderately sized systems. We present a systematic augmentation of the effective core potential basis set of Stevens et al. [J Chem Phys 81, 12 (1984), Can J Chem 70, 612 (1992)] for 39 main group elements based on the procedure used to construct diffuse and polarization functions in the well-known Sadlej basis sets [Collec Czech Chem Comm 53, 1995 (1988)]. Representative calculations have been performed and we have shown that results to within 1% of all-electron calculations using the Sadlej basis set can be obtained for <1-35% of the computational cost using this new basis set.     

Reactivity of V2O3(0001) surfaces: molecular vs dissociative adsorption of water

The adsorption of water on V2O3(0001) surfaces has been investigated by thermal desorption spectroscopy, high-resolution electron energy loss spectroscopy, and X-ray photoelectron spectroscopy with use of synchrotron radiation. The V2O3(0001) surfaces have been generated in epitaxial thin film form on a Rh(111) substrate with three different surface terminations according to the particular preparation conditions. The stable surface in thermodynamic equilibrium with the bulk is formed by a vanadyl (VO) (1x1) surface layer, but an oxygen-rich (radical3xradical3)R30 degrees reconstruction can be prepared under a higher chemical potential of oxygen (microO), whereas a V-terminated surface consisting of a vanadium surface layer requires a low microO, which can be achieved experimentally by the deposition of V atoms onto the (1x1) VO surface. The latter two surfaces have been used to model, in a controlled way, oxygen and vanadium containing defect centres on V2O3. On the (1x1) V=O and (radical3xradical3)R30 degrees surfaces, which expose only oxygen surface sites, the experimental results indicate consistently that the molecular adsorption of water provides the predominant adsorption channel. In contrast, on the V-terminated (1/radical3x1/radical3)R30 degrees surface the dissociation of water and the formation of surface hydroxyl species at 100 K is readily observed. Besides the dissociative adsorption a molecular adsorption channel exists also on the V-terminated V2O3(0001) surface, so that the water monolayer consists of both OH and molecular H2O species. The V surface layer on V2O3 is very reactive and is reoxidised by adsorbed water at 250 K, yielding surface vanadyl species. The results of this study indicate that V surface centres are necessary for the dissociation of water on V2O3 surfaces.     

Adsorption of organosilanes at a Zn-terminated ZnO (0001) surface: molecular dynamics study

Four different organosilanes (octyltrihydroxysilane, butyltrihydroxysilane, aminopropyltrihydroxysilane, and thiolpropyltrihydroxysilane) adsorbed at a reconstructed Zn-terminated polar ZnO (0001) surface are studied via constant temperature (298 K) molecular dynamics simulations. Both single adsorbed silane molecules as well as adsorbed silane layers are modeled, and the energy, distance, orientation, and alignment of these adsorbates are analyzed. The adsorbed silane molecules exhibit behavior depending on the chemical nature of their tail (nonpolar or polar) as well as on the silane concentration at the solid surface (single adsorption or silane layer). In contrast to the O-terminated ZnO surface studied previously, now adsorption can only occur at the vacancies of this reconstructed crystal surface, thus leading to an arched structure of the liquid phase near the crystal surface. Nevertheless, both nonpolar and polar single adsorbed silanes show a similar orientation and alignment at the surface (orthogonal in the former, parallel in the latter case) as for the O-terminated ZnO surface, although the interaction energy with the surface is considerably increased for nonpolar silanes while it is nearly unaffected for the polar ones. For adsorbed silanes within silane layers, the difference to single adsorbed silanes depends on the polarity of the tail: nonpolar silanes again show an orthogonal alignment, while polar silanes exhibit two different orientations at the solid surface-a head and a tail down configuration. This leads to two completely different but nevertheless stable orientations of these silanes at the Zn-terminated ZnO surface.     

Preparation and characterisation of hydroxide stabilised ZnO(0001)-Zn-OH surfaces

Two different approaches under ambient conditions were developed for the preparation of clean, non-reconstructed, single crystalline ZnO(0001)-Zn surfaces. The surface preparation by a wet chemical etching procedure was compared with the same treatment in combination with a subsequent heat treatment in humidified oxygen atmosphere. Depending on the preparation technique, atomically flat terraces with a width of 100 nm to several micrometers were observed using an atomic force microscope (AFM). The obtained surface structures were further characterized by means of angle resolved X-ray photoelectron spectroscopy (AR-XPS), time-of-flight secondary ion mass spectroscopy (ToF-SIMS), Auger electron spectroscopy (AES) and low energy electron diffraction (LEED) measurements. Based on these results it is shown that the obtained surfaces are, in contrast to surfaces prepared under UHV conditions, stabilised by the adsorption of a monolayer of hydroxides. The important role of H(2)O during the heat treatment is pointed out by comparing the results of the same heat treatment in the absence of water. H(2)O turned out to play an important role in the reorganization process of the surface at elevated temperatures, thereby yielding extremely large atomically flat terraces. The terminating edges of these terraces were found to include 120 degrees and 60 degrees angles, thus perfectly reflecting the hexagonal surface structure.     

Self-localization of polyacrylic acid molecules on polar ZnO(0001)-Zn surfaces

The adsorption of single polyacrylic acid (PAAc) molecules was investigated on stepped hydroxide-stabilized polar ZnO(0001)-Zn surfaces using atomic force microscope (AFM) topography and force distance spectroscopy. Stepped surfaces of ZnO(0001)-Zn were prepared by a wet chemical etching procedure and PAAc molecules were adsorbed from aqueous NaClO(4) solutions. AFM single molecule topography studies could be utilized to show that polyacrylic acid molecules specifically adsorb on the non-polar (10-10) step edge faces at low ionic strengths. The radius of gyration of the dissolved PAAc in aqueous solution was measured by means of static light scattering experiments yielding a radius of gyration of R(g)=136 nm at pH 7.4 in 50 mM NaClO(4)/NaOH solution, which is in good agreement with the size of the adsorbed PAAc molecules as measured using AFM. The obtained results could be rationalized in terms of binding-site configurations at step edges and the effect of the chemical environment on both local electric double layer charge and molecular conformation of the PAAc molecules. The point of zero charge of the ZnO(10-10) surface was measured with chemical force microscopy to be pH(PZC)=10.2 ± 0.2. The specific adsorption of polyacrylic acid at non-polar ZnO step-edges can be explained by coordinative bonds formed between the carboxylic acid group and the Zn-surface atoms. On the hydroxide stabilized polar surface only weak hydrogen bonds can be formed in addition to van-der-Waals forces. Thus a "diffusion and trapping" mechanism keeps the adsorbed PAAc molecules mobile on the ZnO(0001)-Zn surface terraces due to small interaction forces until they are trapped at the (10-10) step faces by stronger coordinative bonds from the carboxylic groups to zinc atoms located in the first atomic layer of the crystal structure.     

Properties of the CdSe(0001), (0001), and (1120) single crystal surfaces: Relaxation, reconstruction, and adatom and admolecule adsorption

Details of the chemical mechanism underlying the growth of colloidal semiconductor nanocrystals remain poorly understood. To provide insight into the subject, we have preformed a comprehensive study of the polar (0001) and (0001) and nonpolar (1120) wurtzite CdSe surfaces that are exposed during crystal growth using first-principles density functional theory (DFT-GGA) calculations. Stabilization of these surfaces by relaxation and reconstruction was considered. Two particular reconstructions of the polar surfaces were examined: vacancy formation on a 2 x 2 unit cell and addition of Se and Cd atoms on the (0001) and (0001) surfaces, respectively. Calculation results indicate that the (1120) is the most stable surface when compared to the two polar surfaces. Furthermore, reconstructions of the (0001) surface are energetically favored when compared to reconstructions of the (0001) facet. Adsorption of Cd and Se atoms and the CdSe molecule on the three relaxed surfaces and two reconstructed (0001) surfaces were also investigated. Several binding sites were considered to determine the most stable binding geometries and energetics. Atomic species preferentially bind in either 2-fold or 3-fold sites, while the CdSe molecule binds parallel to the surface on all of the considered surfaces. Vibrational frequencies of the adspecies were calculated for the most stable binding configurations and were included in the zero point energy correction. Diffusion barriers for the atomic and molecular species were estimated where possible to be between 0.2 and 0.4 eV on the three relaxed surfaces. Thermochemistry of the CdSe molecule binding and dissociation was also investigated. On all considered surfaces, dissociation is preferred to desorption with dissociation only exothermic on the (0001) surface. Comparison of the three relaxed and two reconstructed surfaces indicates that CdSe molecule binding and dissociation is thermodynamically favored on the (0001) surface. This implies that under a reaction-controlled regime, the rate of homoepitaxy would be faster on the (0001) Se terminated surface than on the (0001) and (1120) surfaces, making the (0001) surface of a nanocrystal the primary direction of growth.     

CO在Pt(111)和Pt-M(111)(M=Ni,Mg)表面吸附的理论研究

采用密度泛函理论与周期性平板模型相结合的方法,对CO在Pt(111)表面top,fcc,hcp和bridge 4个吸附位和Pt-M(111)(M=Ni,Mg)表面h-top,M-top,Pt(M)Pt-bridge,Pt(M)M-bridge,Pt(Pt)M-bridge,M(Pt)M-bridge,Pt1M2-hcp...     

Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes

We present a set of effective core potential (ECP) basis sets for rhodium atoms which are of reasonable size for use in electronic structure calculations. In these ECP basis sets, the Los Alamos ECP is used to simulate the effect of the core electrons while an optimized set of Gaussian functions, which includes polarization and diffuse functions, is used to describe the valence electrons. These basis sets were optimized to reproduce the ionization energy and electron affinity of atomic rhodium. They were also tested by computing the electronic ground state geometry and harmonic frequencies of [Rh(CO)₂μ‐Cl]₂, Rh(CO)₂ClPy, and RhCO (neutral and its positive, and negative ions) as well as the enthalpy of the reaction of [Rh(CO)₂μ‐Cl]₂ with pyridine (Py) to give Rh(CO)₂ClPy, at different levels of theory. Good agreement with experimental values was obtained. Although the number of basis functions used in our ECP basis sets is smaller than those of other ECP basis sets of comparable quality, we show that the newly developed ECP basis sets provide the flexibility and precision required to reproduce a wide range of chemical and physical properties of rhodium compounds. Therefore, we recommend the use of these compact yet accurate ECP basis sets for electronic structure calculations on molecules involving rhodium atoms. © 2012 Wiley Periodicals, Inc.     

A theoretical study on the pure and doped ZnO nanoclusters as effective nanobiosensors for 5-fluorouracil anticancer drug adsorption

The electronic sensitivity and effectiveness of the pristine, Fe,- Mg-, Al- and Ga-doped ZnO nanoclusters interacted with 5-fluorouracil (5-FU) anticancer drug are theoretically investigated in the gas phase using the B3LYP/wB97XD density functional theory calculations with LANL2DZ basis set. It is concluded that 5-FU adsorption on the doped nanoclusters has relatively higher adsorption energy as compared with the pristine zinc oxide. A number of thermodynamic parameters, such as band gap energy (E_g), adsorption energy (E_ad), molecular electrostatic potential, global hardness (η) and density of electronic states, are attained and compared. Also, calculated geometrical parameters and electronic properties for the studied systems indicate that Mg- and Ga-doped Zn₁₂O₁₂ present higher sensitivity to 5-FU compared with the pristine nanocluster. Theoretical results reveal that adsorption of 5-FU on the doped nanoclusters is influenced by the electronic conductance of the nanocluster. Therefore, Mg- and Ga-doped ZnO can be considered as promising nanobiosensors for detection of 5-FU in medicine.     

Combined theoretical and experimental study on the adsorption of methanol on the ZnO(1010) surface

The structure, dynamics, and energetics of methanol adlayers on the nonpolar ZnO(1010) surface have been studied by He-atom diffraction (HAS), high-resolution electron energy loss spectroscopy (HREELS), thermal desorption spectroscopy (TDS), and density functional calculations. The experimental and theoretical data consistently show that at temperatures below 357 K methanol forms an ordered adlayer with a (2 × 1) periodicity and a coverage of one monolayer in which half of the methanol molecules are dissociated. The ordering of the methanol molecules is governed by repulsive interactions between the methyl groups of the methanol molecules. This repulsive interaction is also responsible for the formation of a second, low-density phase at higher temperatures with half monolayer coverage of undissociated methanol which is stable up to 440 K.     

Molecular adsorption on ZnO(1010) single-crystal surfaces: morphology and charge transfer

While ZnO has excellent electrical properties, it has not been widely used for dye-sensitized solar cells, in part because ZnO is chemically less stable than widely used TiO(2). The functional groups typically used for surface passivation and for attaching dye molecules either bind weakly or etch the ZnO surface. We have compared the formation of molecular layers from alkane molecules with terminal carboxylic acid, alcohol, amine, phosphonic acid, or thiol functional groups on single-crystal zinc oxide (1010) surfaces. Atomic force microscopy (AFM) images show that alkyl carboxylic acids etch the surface whereas alkyl amine and alkyl alcohols bind only weakly on the ZnO(1010) surface. Phosphonic acid-terminated molecules were found to bind to the surface in a heterogeneous manner, forming clusters of molecules. Alkanethiols were found to bind to the surface, forming highly uniform monolayers with some etching detected after long immersion times in an alkanethiol solution. Monolayers of hexadecylphosphonic acid and octadecanethiol were further analyzed by Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and electrochemical measurements. AFM scratching shows that thiols were bound strongly to the ZnO surface, suggesting the formation of strong Zn-S covalent bonds. Surprisingly, the tridentate phosphonic acids adhered much more weakly than the monodentate thiol. The influence of organic grafting on the charge transfer to ZnO was studied by time-resolved surface photovoltage measurements and electrochemical impedance measurements. Our results show that the grafting of thiols to ZnO leads to robust surfaces and reduces the surface band bending due to midgap surface states.     

Hydrogen adsorption on graphite (0001) surface: a combined spectroscopy-density-functional-theory study

The adsorption of H/D atoms on the graphite (0001) surface is investigated by means of both high-resolution electron-energy loss spectroscopy (HREELS) and periodic first-principle density-functional theory. The two methods converge towards two modes of adsorption: adsorption in clusters of about four hydrogen atoms and adsorption in pairs of atoms on contiguous carbon sites. The desorption energies estimated from the calculated dissociation energies range from 8 to 185 kJ mol(-1) leading to an estimated surface coverage at saturations of 30-44 at. %. These results are compared with previous thermal desorption spectroscopy results. New HREEL signal assignments are proposed based on quantum calculations.     

H2O and H2 interaction with ZnO surfaces: A MNDO,AM1, and PM3 theoretical study with large cluster models

We investigated the adsorption and heterolytic dissociation of H₂O and H₂ molecules on a (ZnO)₂₂ cluster corresponding to ZnO (0001), (000(OVERBAR)1), and (10(OVERBAR)10) surfaces using MNDO , AM 1 and PM 3 semiempirical procedures. The geometry of the adsorbed molecule has been optimized in order to analyze binding energies, charge transfer, and preferential sites of interaction. The adsorbed species interact most strongly when it is bonded to the twofold coordinated zinc atom of the cluster surface. The interaction of the H₂O molecule with the surface of ZnO has a charge transfer from H₂O to the surface ranging between 0.17 and 0.27 au. The neighboring atoms of the surface are the main receptors during the process of charge transfer. Our results indicate that there is a weak bonding of the hydrogen atom from OH with the oxygen surface atom that could produce the O(SINGLE BOND)H·O band. The interaction of the H₂ molecule with the surface is generally weak and only the PM 3 method yields a strong binding energy for this interaction. There is a charge transfer from the H₂ molecule to the surface. The chemisorption of H on oxygen atom of the surface transfer charge from the surface to the H. We also calculated the vibrational analyses for these interactions on ZnO surface and compared our results with available experimental data. © 1996 John Wiley & Sons, Inc.     

A comparative study ofab-initio effective core potential and all-electron calculations for molecular structures and transition states

The reliability of theab-initio effective core potential method for calculating molecular geometries was tested for several polyatomic molecules by using the energy gradient technique. The calculated geometries are in good agreement with those of all-electron calculation not only for equilibrium but also for transition states. The heat of reaction and the activation barrier height compare very well with those of all-electron calculation as well.     

氢原子在Ru(0001)和Ru(1010)面上吸附扩散势能面的结构

本文构造了H-Ru相互作用的五参数Morse势,用经典的对势方法研究了氢原子在Ru(0001)和Ru(1010)面上的吸附和扩散,得到了氢原子在两个表面上的吸附位、吸附几何、结合能及本征振动等数据与实验结果符合得很好;同时研究了两个体系的吸附扩散势能面结构。     

Surface structure of (10(-)10) and (11(-)20) surfaces of ZnO with density functional theory and atomistic simulation

We have calculated the stability of two of the low-index surfaces known to dominate the morphology of ZnO as a function of stoichiometry. These two surfaces are (10(-)10) and (11(-)20). In each case, two terminations only are stable for a significant range of oxygen and hydrogen chemical potential: the pure stoichiometric surface and a surface covered in a monolayer of water. The mode by which the water adsorbs is however different for the two surfaces considered. On the (10(-)10) surface the close proximity of the water molecules means hydrogen bonding can occur between adjacent chemiabsorbed water molecules and hence there is little difference in the stability of the hydrated and hydroxylated surface, and in fact the most stable surface occurs with a combination of dissociated and undissociated water adsorption. In the case of the (11(-)20) surface, it is only when full dissociation has occurred that a hydrogen-bonding network can form. Our results also show good agreement between DFT and atomistic simulations, suggesting that potential based methods can usefully be applied to ZnO.     

A theoretical study on anomalous temperature dependence of pKw of water

pH, with its well-known value of 7 at ambient condition, is a most basic property of water, with wide implications in chemistry and biology. The pH value is determined by the tendency of autoionization of water molecules into ion pairs, H(+) and OH(-), and is expected to vary extensively with the water condition, which determines the stability of the ion pairs. When temperature rises from the normal to the supercritical region, the pH of water experimentally exhibits complex, nonmonotonic temperature dependence, that is, it first decreases from 7 and then increases rapidly. Accurate theoretical evaluation of pH and microscopic understanding of this anomalous behavior have proven to be a challenging task because the hydration of these ions, especially for OH(-), is very difficult to reproduce. In the present study a molecular simulation is performed to understand this peculiar temperature dependence. The imbalance between the ion-water and the water-water molecular interaction strengths and the concomitant water density enhancement in the hydration shell, observed in the supercritical liquids, serve to put a subtle balance to produce this temperature dependence of the pH value. It is found that the large charge transfers from H(+) and OH(-) to the surrounding water molecules take place. In these transfers, not only water molecules in the neighboring hydration shell but also those in the outer hydration shell play a significant role. The coordination number of water molecules around OH(-) is found to be 4.5 at 300 K, which decreases slowly with temperature, for example, 4 at 800 K, in the present calculation.     

Ethanol reforming on Co(0001) surfaces: a density functional theory study

A computational study using density functional theory is carried out to investigate the reaction mechanism of ethanol steam reforming on Co(0001) surfaces. The adsorption properties of the reactant, possible intermediates, and products are carefully examined. The reaction pathway and related transition states are also analyzed. According to our calculations, the reforming mechanism primarily consisting of dehydrogenation steps of ethanol, ethoxy, methanol, methoxy, and formic acid, is feasible on Co(0001) surfaces. It is also found that the reaction of formaldehyde yielding formic acid and hydrogen may not be an elementary reaction. The dehydrogenation of ethoxy possesses the highest barrier and is accordingly identified as the rate-determining step.