Biomedical subjects

Annabella Selloni

Publications and source records attributed to Annabella Selloni.

At least 19 recordsLinked to original sources

PubMed2006

Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers.

We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA-Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.

Journal Article↗

PubMed2006

Side-by-side characterization of electron tunneling through monolayers of isomeric molecules: a combined experimental and theoretical study.

We report a new experimental method for measuring relatively small differences in electron tunneling through two distinct monolayers. We place them side by side using scanning probe nanolithography and compare the tunneling currents by conductive probe atomic force microscopy under identical force, voltage, and tip contamination conditions. We demonstrate the validity of our approach by applying it to two isomeric molecules with similar length and functional groups, with only the position of two functional groups, one aromatic and the other aliphatic, being inverted with respect to each other. The relative values of the two tunneling currents, calculated using density functional theory and the Tersoff-Hamann approach, compare very well with the experimental data, providing us with an example of theory vs experiment agreement that is rather uncommon in this field.

Letter↗

PubMed2006

Origin of photoactivity of nitrogen-doped titanium dioxide under visible light.

Nitrogen-doped titanium dioxide (N-TiO2), a photocatalytic material active in visible light, has been investigated by a combined experimental and theoretical approach. The material contains single-atom nitrogen impurities that form either diamagnetic (Nb-) or paramagnetic (Nb*) bulk centers. Both types of Nb centers give rise to localized states in the band gap of the oxide. The relative abundance of these species depends on the oxidation state of the solid, as, upon reduction, electron transfer from Ti3+ ions to Nb* results in the formation of Ti4+ and Nb-. EPR spectra measured under irradiation show that Nb centers are responsible for visible light absorption with promotion of electrons from the band gap localized states to the conduction band or to surface-adsorbed electron scavengers. These results provide a characterization of the electronic states associated with N impurities in TiO2 and, for the first time, a picture of the processes occurring in the solid under irradiation with visible light.

Journal Article↗

PubMed2006

Electronic structure of defect states in hydroxylated and reduced rutile TiO2(110) surfaces.

It has been experimentally observed that a bridging oxygen vacancy on the rutile TiO2(110) surface introduces localized Ti3+ 3d1 states about 1 eV below the conduction band which are not removed upon dissociation of a water molecule and formation of a pair of hydroxyl groups. Density functional calculations based on pure exchange-correlation functionals have not been able to satisfactorily reproduce and analyze these findings. Here we show that a correct description of the localized defect states on reduced and hydroxylated TiO2(110) is achieved only if proper geometry relaxation is accounted for using hybrid exchange functionals. We confirm the electron trapping nature of Ti(OH) groups but find no evidence that these defects should also act as hole traps by formation of Ti4+(OH)* radicals.

Journal Article↗

PubMed2006

Interface and molecular electronic structure vs tunneling characteristics of CH3- and CF3-terminated thiol monolayers on Au(111).

By means of density functional theory calculations, we investigate work functions, energy level alignments, charge transfers, and tunneling characteristics of CH3- and CF3-terminated alkane- and diphenylthiol monolayers on Au(111). While the alignments of the energy levels and the charge transfers at the metal-molecule interface are found to be determined by the value of the clean Au surface work function relative to the HOMO ionization potential (IP) at the thiolate end of the monolayer, the change of work function for the modified Au(111) surface is dominated by the properties of the thiolate monolayer, including the character, saturated or conjugated, of the molecule and the chemical nature and orientation of the terminal group. The tunneling currents through the adsorbed molecular monolayers are calculated using the Tersoff-Hamann approach. The computed difference between the I-V characteristics for the CH3- and CF3-terminated alkanethiol monolayers agree well with available experimental data. The energy barrier at the metal-molecule interface, the molecular electronic structure, and the IP of the terminal group are the key parameters which determine the tunneling properties.

Journal Article↗

PubMed2006

Steps on anatase TiO2(101).

Surface defects strongly influence the surface chemistry of metal oxides, and a detailed picture of defect structures may help to understand reactivity and overall materials performance in many applications. We report first-principles calculations of step edges, the most common intrinsic defects on surfaces (and probably the predominant ones on nanoparticles). We have determined the structure, energetics, and chemistry of step edges on the (101) surface of TiO(2) anatase, an important photocatalytic material. Scanning tunnelling microscopy measurements of step-edge configurations and the contrast in atomically resolved images agree remarkably well with the theoretical predictions. Step-edge formation energies as well as the adsorption energies of water scale with the surface energy of the step facet, a trend that is expected to generally hold for metal oxide surfaces. Depending on the terrace/step configuration, this can lead to a situation where a step is less reactive than the flat terrace.

Journal Article↗

PubMed2006

Competing mechanisms in the optically activated functionalization of the hydrogen-terminated Si(111) surface.

Recent experiments have shown that organic monolayers on silicon surfaces can be formed through the optically activated surface reaction of H-terminated Si surfaces with terminally unsaturated organic molecules (Eves et al. J. Am. Chem. Soc. 2004, 126, 14318; Sun et al. J. Am. Chem. Soc. 2005, 127, 2514). Possible mechanisms for the formation of this monolayer involve the abstraction of a H atom either at the same attachment site of the molecule (Path A) or from a neighboring site (Path B). Using periodic Density Functional Theory calculations together with an efficient method for finding reaction pathways, we examine both optically activated reaction mechanisms for an alkene and an aldehyde reacting with H-Si(111). Our results show that while Path A is energetically more favorable its significant barrier is likely to limit its viability. Path B on the other hand encounters a much lower H atom abstraction barrier and appears to be more viable.

Journal Article↗

PubMed2006

Density functional theory study of formic acid adsorption on anatase TiO2(001): geometries, energetics, and effects of coverage, hydration, and reconstruction.

We present density functional theory calculations and first-principles molecular dynamics simulations of formic acid adsorption on anatase TiO(2)(001), the minority surface exposed by anatase TiO(2) nanoparticles. A wide range of factors that may affect formic acid adsorption, such as coverage, surface hydration, and reconstruction, are considered. It is found that (i) formic acid dissociates spontaneously on unreconstructed clean TiO(2)(001)-1 x 1, as well as on the highly reactive ridge of the reconstructed TiO(2)(001)-1 x 4 surface; (ii) on both the 1 x 1 and 1 x 4 surfaces, various configurations of dissociated formic acid exist with adsorption energies of about 1.5 eV, which very weakly depend on the coverage; (iii) bidentate adsorption configurations, in which the formate moiety binds to the surface through two Ti-O bonds, are energetically more favored than monodentate ones; (iv) partial hydration of TiO(2)(001)-1 x 1 tends to favor the bidentate chelating configuration with respect to the bridging one but has otherwise little effect on the adsorption energetics; and (v) physical adsorption of formic acid on fully hydrated TiO(2)(001)-1 x 1 is also fairly strong. Comparison of the present results for formic acid adsorption with those for water and methanol under similar conditions provides valuable insights to the understanding of recent experimental results concerning the coadsorption of these molecules.

Adsorption↗

PubMed2005

Combined experimental and DFT-TDDFT computational study of photoelectrochemical cell ruthenium sensitizers.

We report a combined experimental and computational study of several ruthenium(II) sensitizers originated from the [Ru(dcbpyH(2))(2)(NCS)(2)], N3, and [Ru(dcbpyH(2))(tdbpy)(NCS)(2)], N621, (dcbpyH(2) = 4,4'-dicarboxy-2,2'-bipyridine, tdbpy = 4,4'-tridecyl-2,2'-bipyridine) complexes. A purification procedure was developed to obtain pure N-bonded isomers of both types of sensitizers. The photovoltaic data of the purified N3 and N621 sensitizers adsorbed on TiO(2) films in their monoprotonated and diprotonated state, exhibited remarkable power conversion efficiency at 1 sun, 11.18 and 9.57%, respectively. An extensive Density Functional Theory (DFT)-Time Dependent DFT study of these sensitizers in solution was performed, investigating the effect of protonation of the terminal carboxylic groups and of the counterions on the electronic structure and optical properties of the dyes. The calculated absorption spectra are in good agreement with the experiment, thus allowing a detailed assignment of the UV-vis spectral features of the two types of dyes. The computed alignments of the molecular orbitals of the different complexes with the band edges of a model TiO(2) nanoparticle provide additional insights into the electronic factors governing the efficiency of dye-sensitized solar cell devices.

Journal Article↗

PubMed2005

First-principles studies of vanadia-titania catalysts: beyond the monolayer.

Periodic density functional calculations have been used to investigate the structure and stability of epitaxial vanadium oxide films grown on the TiO(2)(001) anatase surface. The formation energy of films of V(2)O(5) stoichiometry, initially low, is found to rapidly increase with the film thickness, at variance to what is obtained for reduced pseudomorphic VO(2) films. This is in tune with results of oxygen-assisted molecular beam epitaxy. The oxidation of thick, viz. >2 monolayers (ML), VO(2) films yields a c(2 x 2) reconstructed surface, in agreement with low energy electron diffraction. These films are composed by partially reduced inner V atoms in a distorted-octahedral environment, and by isolated surface dioxovanadium centers exhibiting a distorted trigonal-bipyramidal coordination. Single scattering simulations of X-ray photoelectron diffraction patterns have also been performed, taking both 2- and 3-ML surface surface-oxidized films as models. Results are in fair agreement with experiments referring to films grown in oxidizing conditions, which suggests that coherent vanadia ultrathin films could be formed in vanadia-titania catalysts. The electronic structure of the films has been finally studied, finding that the terminal oxygens carried by the surface dioxovanadium species have a strong nucleophilic character, which makes them potential active centers for selective oxidation catalysis.

Journal Article↗

PubMed2005

O2 interaction and reactivity on a model hydroxylated rutile(110) surface.

Recently several theoretical studies have examined oxygen adsorption on the clean, reduced TiO2(110) surface. However the photocatalytic behavior of TiO2 and the scavenging ability of oxygen are known to be influenced by the presence of surface hydroxyls. In this paper the chemistry of O2 on the hydroxylated TiO2 surface is investigated by means of first-principles total energy calculations and molecular dynamics (MD) simulations. The MD trajectories show a direct, spontaneous reaction between O2 and the surface hydroxyls, thus supporting the experimental hypothesis that the reaction does not necessarily pass through a chemisorbed O2 state. Following this reaction, the most stable chemisorbed intermediates are found to be peroxide species HO2 and H2O2. Although these intermediates are very stable on the short time scale of MD simulations, the energetics suggests that their further transformation is connected to a new 300 K feature observed in the experimental water temperature programmed desorption (TPD) spectrum. The participation of two less stable intermediate states, involving terminal hydroxyls and/or chemisorbed water plus oxygen adatoms, to the desorption process, is not supported by the total energy calculations. Analysis of the projected density of states, however, suggests the possibility that these intermediates have a role in completing the surface oxidation immediately before desorption.

Journal Article↗

PubMed2005

Reactivity of anatase TiO(2) nanoparticles: the role of the minority (001) surface.

Methanol adsorption on clean and hydrated anatase TiO(2)(001)-1 x 1 is studied using density functional theory calculations and first principles molecular dynamics simulations. It is found that (i) dissociative adsorption is favored on clean TiO(2)(001) at both low and high methanol coverages; (ii) on the partially hydrated surface, methanol dissociation is not affected by the coadsorbed water and can still occur very easily; (iii) the dissociative adsorption energy of methanol is always larger than that of water under similar conditions. This implies that water replacement by methanol is energetically favored, in agreement with recent experimental observations on colloidal anatase nanoparticles.

Models, Molecular↗

PubMed2005

Role of molecular conjugation in the surface radical reaction of aldehydes with H-Si(111): first principles study.

Within the current effort to understand and develop the organic functionalization of silicon surfaces, recent experiments have identified the radical chain reaction of unsaturated organic molecules with H-terminated silicon surfaces as a particularly promising route for controlled formation of such functionalized surfaces. Using periodic density functional theory calculations, we theoretically study and characterize the basic steps of the radical chain reaction mechanism for different aldehyde molecules (formaldehyde, benzaldehyde, propanaldehyde, propenaldehyde) reacting with the H-Si(111) surface, under the assumption that a Si dangling bond is initially present on the surface. Molecular conjugation is found to play a crucial role in the viability of the reaction, by controlling the delocalization of the spin density at the reaction intermediate. Interesting differences between our present results for aldehydes and our previous study for the reactions of alkene/alkyne molecules with H-Si(111) are observed and discussed (Takeuchi et al. J. Am. Chem. Soc. 2004, 126, 15890).

Journal Article↗

PubMed2005

O2 and vacancy diffusion on rutile(110): pathways and electronic properties.

The binding structures and diffusion pathways of molecular oxygen on a defective TiO2(110) surface are studied by means of a recently developed first-principles string molecular dynamics approach. A variety of molecular and dissociated O2 adsorption states are identified and the kinetics of their interconversion is analyzed. These results, as well as calculations of the electronic properties and of scanning tunneling microscopy (STM) images, are used to discuss recent experimental observations of the interactions between surface oxygen vacancies and the adsorbed oxygen molecule.

Computer Simulation↗

PubMed2005

Electron tunneling through molecular media: a density functional study of Au/Dithiol/Au systems.

We report a density functional theory study of the electronic properties of n-alkanedithiols (CnS2, with n=4, 8 and 12) sandwiched between two Au(111) infinite slab electrodes. We investigate the influence of the distance between the two electrodes and of the molecular chain length, tilt angle, and coverage on the local density of states (LDOS) at the Fermi energy (E(f)). We find that the (small) value of the LDOS at Ef near the center of the molecular wires--a quantity that is related to the tunneling current--is mainly determined by the length n of the alkane chains: it originates from the tails of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) which are broadened by the interaction with the electrodes, and decays exponentially with the length of the molecular wire. This opens a nonresonance tunneling channel for charge transport at small bias voltages. While the length of the hydrocarbon chain appears to be the determining factor, the tilt angle of the molecular wires with respect to the electrode surfaces, and therefore the distance between these, has a small influence on the LDOS at the center of the molecule, while the effect of coverage can be ignored. The picture which emerges from these calculations is totally consistent with a through-bond tunneling mechanism.

Alkanes↗

PubMed2005

A theoretical study of biotin chemisorption on Si-SiC(001) surfaces.

Biotin is a promising candidate for functionalization of semiconducting surfaces, given its strong, unmatched affinity to specific proteins such as streptavidin and avidin. Using density functional theory, we have carried out a theoretical investigation of the structural and electronic properties of biotin chemisorbed on a biocompatible substrate; in particular we have considered the clean and hydroxylated Si-SiC(001) surfaces. Our calculations show that, upon chemisorption, biotin retains the electronic properties responsible for its strong affinity to proteins. While the electronic states of the hydroxylated surface undergo negligible changes in the presence of the molecule, those of the clean surface are considerably affected.

Adsorption↗

PubMed2005

Adsorption of water on reconstructed rutile TiO2(011)-(2 x 1): Ti=O double bonds and surface reactivity.

Recent combined experimental and theoretical studies (Beck et al., Phys. Rev. Lett. 2004, 93, 036104) have provided evidence for Ti=O double-bonded titanyl groups on the reconstructed rutile TiO(2)(011)-(2 x 1) surface. The adsorption of water on the same surface is now investigated to further probe the properties of these groups, as well as to confirm their existence. Ultraviolet photoemission experiments show that water is adsorbed in molecular form at a sample temperature of 110 K. At the same time, the presence of a 3sigma state in the photoemission spectra and work function measurements indicate a significant amount of hydroxyls within the first monolayer of water. At room temperature, scanning tunneling microscopy (STM) suggests that dissociated water is present, and about 30% of the surface active sites are hydroxylated. These findings are well explained by total energy density functional theory calculations and Car-Parrinello molecular dynamics simulations for water adsorption on the titanyl model of TiO(2)(011)-(2 x 1). The theoretical results show that a mixed molecular/dissociative layer is the most stable configuration in the monolayer regime at low temperatures, while complete dissociation takes place at 250 K. The arrangement of the protonated mono-coordinated oxygens in the mixed molecular/dissociated layer is consistent with the observed short-range order of the hydroxyls in the STM images.

Journal Article↗

PubMed2005

Density functional theory study of one-dimensional growth of styrene on the hydrogen-terminated Si(001)-(3 x 1) surface.

Recent experimental work has shown that the addition of styrene molecules to hydrogen-terminated Si(001) surfaces leads to the formation of one-dimensional molecular structures through a radical-initiated surface chain reaction mechanism. These nanometric structures are observed to be directed parallel to the dimer rows on the H-Si(001)-(2 x 1) surface and perpendicular to the same rows on H-Si(001)-(3 x 1). Using periodic density functional theory (DFT) calculations, we have studied the initial steps of the radical chain mechanism on the H-Si(001)-(3 x 1) surface and compared them to analogous results for H-Si(001)-(2 x 1). On the H-Si(001)-(3 x 1) surface, one of the crucial steps of the surface chain reaction, namely, the abstraction of a H atom from a nearby surface hydride unit, is found to have a somewhat smaller activation energy in the direction perpendicular to the dimer rows (H abstraction from the nearest dihydride site) than along the rows (H abstraction from a neighboring dimer). Additionally, due to the steric repulsion between the styrene molecules and the SiH2 subunits, growth along the dimer rows is not thermodynamically favorable on the (3 x 1) surface. On the other hand, due to the absence of the SiH2 subunits, growth parallel to the Si dimer rows becomes favored on the H-Si(001)-(2 x 1) surface.

Journal Article↗