Vlasta Bonacic-Koutecky

Ab initio study of the absorption spectra of Agn (n=5–8) clusters

The absorption spectra of Ag5–8 have been determined in the framework of the linear response equation-of-motion coupled cluster method and related techniques employing 11-electron relativistic effective core potential. In these treatments electron correlation effects for 11 electrons per atom are included, providing an accurate description of excited states of silver clusters. The calculations of transition energies and oscillator strengths have been carried out in a large energy interval for the stable structures and for the isomeric forms higher in energy. This allowed us to investigate the influence of structural properties on the spectroscopic patterns and to determine the role of d-electrons. Inclusion of d-electrons in the correlation treatment is mandatory to obtain accurate values for transition energies, but the excitations of s-electrons are primarily responsible for the spectroscopic patterns. They are characterized by the interference phenomena known in molecular spectroscopy which lead to a s...

Influence of Charge State on Catalytic Oxidation Reactions at Metal Oxide Clusters Containing Radical Oxygen Centers

Evidence obtained by guided-ion-beam mass spectrometry experiments and density functional theory calculations indicates that by adding one oxygen atom with a full octet of valence electrons (O(2-)) to stoichiometric cationic zirconium oxide clusters (ZrO(2))(x)(+) (x = 1-4), a series of anionic clusters (Zr(x)O(2x+1))(-) (x = 1-4) are formed which contain radical oxygen centers with elongated (elongation approximately 0.24 +/- 0.02 A) metal-oxygen bonds. These anionic clusters oxidize carbon monoxide, strongly associate acetylene, and weakly associate ethylene, in contrast to the cationic species which were found previously to be highly active toward the oxidation of all three molecules. Theoretical investigations indicate that a critical hydrogen transfer step necessary for the oxidation of ethylene and acetylene at metal oxide clusters containing radical oxygen centers is energetically favorable for cationic clusters but unfavorable for the corresponding anionic species. The calculated electrostatic potential of the cluster reveals that in the case of cations, a favorable interaction with nucleophilic molecules takes place over the whole surface of the (ZrO(2))(x)(+) (x = 1-4) clusters, compared to a restricted interaction of ethylene and acetylene with the less coordinated zirconium atom in the case of the anionic (Zr(x)O(2x+1))(-) (x = 1-4) species. Therefore, in spite of the common presence of a radical oxygen center in specific anionic and cationic stoichiometries, the extent to which various classes of reactions are promoted is influenced by charge state. Moreover, the (Zr(x)O(2x+1))(-) (x = 1-4) series of anionic clusters may be regenerated by reacting oxygen deficient clusters with a strong oxidizer. This indicates that not only cationic species, as shown previously, but also anionic clusters may promote multiple cycles of carbon monoxide oxidation.

Nonadiabatic dynamics within time-dependent density functional tight binding method.

A nonadiabatic molecular dynamics is implemented in the framework of the time-dependent density functional tight binding method (TDDFTB) combined with Tullys stochastic surface hopping algorithm. The applicability of our method to complex molecular systems is illustrated on the example of the ultrafast excited state dynamics of microsolvated adenine. Our results demonstrate that in the presence of water, upon initial excitation to the S(3) (pi-pi*) state at 260 nm, an ultrafast relaxation to the S(1) state with a time constant of 16 fs is induced, followed by the radiationless decay to the ground state with a time constant of 200 fs.

Probing the Electronic Structure and Chemical Bonding of Gold Oxides and Sulfides in AuOn− and AuSn− (n = 1, 2)

The Au-O and Au-S interactions are essential in nanogold catalysis and nanotechnology, for which monogold oxide and sulfide clusters serve as the simplest molecular models. We report a combined photoelectron spectroscopy and ab initio study on AuO (-) and AuO 2 (-) and their valent isoelectronic AuS (-) and AuS 2 (-) species to probe their electronic structure and to elucidate the Au-O and Au-S chemical bonding. Vibrationally resolved spectra were obtained at different photon energies, providing a wealth of electronic structure information for each species. Similar spectra were observed for AuO (-) and AuS (-) and for the linear OAuO (-) and SAuS (-) species. A bent isomer was also observed as Au(S 2) (-) in the AuS 2 (-) spectra, whereas a similar Au(O 2) (-) complex was not observed in the case of AuO 2 (-). High-level ab initio calculations were conducted to aid spectral assignments and provide insight into the chemical bonding in the AuX (-) and AuX 2 (-) molecules. Excellent agreement is achieved between the calculated electronic excitations and the observed spectra. Configuration interactions and spin-orbit couplings were shown to be important and were necessary to achieve good agreement between theory and experiment. Strong covalent bonding was found in both the AuX (-) and the XAuX (-) species with multiple bonding characters. While Au(S 2) (-) was found to be a low-lying isomer with a significant binding energy, Au(O 2) (-) was shown to be unbound consistent with the experimental observation. The latter is understood in the context of the size-dependent reactivity of Au n (-) clusters with O 2.

Optical and structural properties of copper-oxytocin dications in the gas phase.

We present a joint experimental and theoretical investigation of the structural and optical properties of copper-oxytocin dications in the gas phase. Ion mobility and UV photodissociation experiments were performed, allowing the investigation of the influence of the Cu(2+) ion on the structural and optical properties of oxytocin. Density functional theory calculations were performed to find low energy structures for the bare and complexed peptide and to characterize optical spectral features. Copper complexation induces a drastic change in the structure of the oxytocin peptide. In particular, we predict a 4N chelation of the copper cation which leads to a contraction of the oxytocin ring. The gas phase lowest-energy structures are compared with the X-ray crystal structure of the oxytocin molecule bound to its receptor protein. The optical spectrum of oxytocin complexed with the copper cation displays a global enhancement of the photofragmentation yield as compared to the one recorded for the doubly protonated oxytocin. Moreover, experimental and calculated optical spectra of protonated tyrosine have also been determined, since its leading features are present in oxytocin as well.

Semiclassical calculations of the cross section for electron-impact ionization of

The semiclassical Deutsch - Mark (DM) formalism for the calculation of absolute cross sections for the single ionization of atoms has been extended to the calculation of the total single ionization cross section of the fullerene . The present calculation uses a Mulliken population analysis in which the outermost 120 orbitals are represented as linear combinations of the atomic C(2s) and C(2p) orbitals and no contributions from the more tightly bound C(1s) electrons have been considered. Detailed comparisons are made with available experimental data. Calculated cross sections are considerably larger (and the cross section curve slightly different in shape) than the measured ones. This indicates that the DM formalism (along with other calculation schemes based on an additivity concept) cannot without appropriate corrections be applied to targets with a complex structure such as .

UV photodissociation of proline-containing peptide ions: insights from molecular dynamics.

ABSTRACTUV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S2 and S3, lie close to 213 nm. Non-adiabatic MD simulation starting from S2 and S3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments. Graphical Abstractᅟ

Theoretical determination of the absolute electron impact ionization cross-section function for silver clusters Agn (n=2–7)

A recently developed semiclassical approach (DM formalism) was used to calculate the absolute total electron-impact single ionization cross sections for silver clusters Agn (n=2–7) from threshold to 1000 eV. Similar to other cluster properties, a clear odd–even effect has been observed for the calculated cross sections and is ascribed to the effective electron numbers in the valence shell. The only available experimental data for comparison are partial cross sections for the production of the singly charged parent ions for the monomer up to the tetramer. No experimental data are available as yet for any larger clusters nor for the total ionization cross sections. Nevertheless, a comparison of the results of the present calculations with calculations using additivity rules applied to molecules and clusters gives valuable insight into the ionization behavior of clusters as a function of cluster size and thus elucidates the transition from a molecular-type situation where the cross sections of the constituen...

Silver cluster chromophores for absorption enhancement of peptides.

We present a theoretical study of the structural and optical properties of tripeptide-silver cluster hybrid systems which shows that silver clusters induce significant absorption enhancement in the spectral region between 225 and 350 nm with respect to the pure peptide. This allows the use of clusters as chromophores for absorption enhancement of peptides and proteins and offers a potential for different applications in biosensing. Furthermore, we demonstrate that cluster binding can change the conformational preference for the secondary structure type leading possibly to new functional properties.