Photoelectron spectroscopy on thin films of extended zinc porphyrazines

Photoemission measurements were performed on a series of stepwise benzoannelated zinc porphyrazine molecules in thin films. The electronic structure of tert-butyl-substituted zinc tetraazaporphyrin, phthalocyanine, and naphthalocyanine is investigated using mainly EUV synchrotron radiation. A detailed analysis of the zinc satellites in the spectra of the valence region is performed in an attempt to infer the effect of ligand size extension on the metal-ligand interactions. No differences in the character of the bond between zinc and ligand were detected as a function of ligand size. The results are compared with those for the respective metal-free and copper-containing molecules.     

Proton transfer in ammonia cluster cations: molecular dynamics in a self consistent field

A theoretical study of the energetics and intramolecular dynamics for ammonia cluster cations (NH₃) ₂ ⁺ and (NH₃) ₃ ⁺ is presented. The proton transfer mechanism after a vertical ionisation is followed in detail. Structural and energetic calculations are performed near the Hartree-Fock self consistent field (HF-SCF) limit; all open shell calculations are spin restricted (RHF). The calculations reconcile experimental results from thermochemical and photoionisation measurements: discrepancies in the energetics are shown to be due to the probing of different regions of the potential energy surface (PES). For the dynamics calculations, it is impractical to determine a large region of the multidimensional PES and then integrate Newton's equations. The calculations therefore incorporate a quantum mechanical determination of the electronic energy of the system after each time increment while nuclear degrees of freedom are handled classically. In this way, the classical reaction path across the Born-Oppenheimer surface is obtained.     

Electron binding energies of aqueous alkali and halide ions: EUV photoelectron spectroscopy of liquid solutions and combined ab initio and molecular dynamics calculations

Photoelectron spectroscopy combined with the liquid microjet technique enables the direct probing of the electronic structure of aqueous solutions. We report measured and calculated lowest vertical electron binding energies of aqueous alkali cations and halide anions. In some cases, ejection from deeper electronic levels of the solute could be observed. Electron binding energies of a given aqueous ion are found to be independent of the counterion and the salt concentration. The experimental results are complemented by ab initio calculations, at the MP2 and CCSD(T) level, of the ionization energies of these prototype ions in the aqueous phase. The solvent effect was accounted for in the electronic structure calculations in two ways. An explicit inclusion of discrete water molecules using a set of snapshots from an equilibrium classical molecular dynamics simulations and a fractional charge representation of solvent molecules give good results for halide ions. The electron binding energies of alkali cations computed with this approach tend to be overestimated. On the other hand, the polarizable continuum model, which strictly provides adiabatic binding energies, performs well for the alkali cations but fails for the halides. Photon energies in the experiment were in the EUV region (typically 100 eV) for which the technique is probing the top layers of the liquid sample. Hence, the reported energies of aqueous ions are closely connected with both structures and chemical reactivity at the liquid interface, for example, in atmospheric aerosol particles, as well as fundamental bulk solvation properties.     

GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5,730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms.     

Convexity in finite metric spaces

A subsetS of a metric space (X,d) is calledd-convex if for any pair of pointsx,y S each pointz X withd(x,z) +d(z,y) =d(x,y) belongs toS. We give some results and open questions concerning isometric and convexity-preserving embeddings of finite metric spaces into standard spaces and the number ofd-convex sets of a finite metric space.     

Coherence effects in low energy Na*(3p)+Na+ scattering: Experiment and semiclassical calculations

Pronounced polarization effects have been observed in inelastic collisions of laser state-prepared Na^*(3p,M _L) with Na⁺ leading to Na^*(3d) for the energy rangeE _CM=20–45 eV. Using linearly polarized light the dependence of the inelastic process on the alignment of the electronic charge cloud of the Na^*(3p) prior to the collision has been measured. In studies with left and right hand circularly polarized light the angular momentum transferred in the collision process has been determined. The results are compared with similar data for the 3p→3s deexitation process studied previously [6]. The density matrix of the Na^*(3p) state has been evaluated with respect to the collisional excitation to Na^*(3d). Semiclassical calculations based on the coupled channel impact parameter approximation using pseudopotentials [7] and nonadiabatic rotational coupling elements for the Na ₂ ^* system [12] have been performed. The agreement with the experimental results is good, in particular for the higher collision energies.     

Alignment and orientation effects in resonant charge exchange from laser excited Na*(3p)

A collisional alignment and orientation study with planar symmetry is described, determining the complete density matrix for resonant charge transfer from laser excited atoms. Results are reported for the Na⁺+Na*(3p) system over the collision energy rangeE _c.m.=50?100 eV. We communicate the optimal alignment angle γ and linear polarisationP _l ⁺ of the charge cloud as well as its relative height ρ₀₀ and the angular momentumL _⊥ ⁺ transferred in the collision as a function of the scattering angle. For preparation of the sodium 3p orbital in the scattering plane (positive reflection symmetry) we observe that at small reduced scattering angles (<20 eV°) the preparation of apσ at large internuclear distances contributes most to the scattering intensity whereas at larger reduced scattering angles (>60 eV°) apπ⁺ preparation is more important. In contrast, preparation of thepπ^? orbital (perpendicular to the scattering plane) is large at small and vanishes at larger scattering angles. We conclude that orbital following cannot be assumed in this resonant charge transfer process. The angular momentum transfer is observed to be small, indicating only little coherence in the process, but shows nevertheless an interesting behaviour as a function of scattering angle.     

Reactive scattering of sodium clusters with molecular oxygen

The first reactive differential scattering study for atomic clusters is reported. Oxidation of Na _x (x8) with O₂ is investigated in a crossed beam apparatus. Sodium oxide (Na _n O,n4) and sodium dioxide (Na _n O₂,n6) are produced with a total reactive cross section from 50 to 80 Ų, depending on the cluster size. The excess energies for these reactions are estimated by an SCF type ab initio calculation and range from 0.5 to 5 eV. The large cross section may then be understood quantitatively in terms of a harpooning mechanism as a first step in the reaction path. Angular distributions have been determined for the most abundant products, showing strong forward scattering. Two different schemes are discussed for the reaction: while the dioxides Na _n O₂ may be formed by an evaporative cooling process from a highly excited collision complex, formation of Na _n O appears to originate from a direct process. In both cases the experimental data suggest that most of the exothermicity remains in the reaction products.     

Fragmentation dynamics of ammonia cluster ions after single photon ionisation

A reflecting time of flight mass spectrometer (RETOF) is used to study unimolecular and collision induced fragmentation of ammonia cluster ions. Synchrotron radiation from the BESSY electron storage ring is used in a range of photon energies from 9.08 up to 17.7 eV for single photon ionisation of neutral clusters in a supersonic beam. The threshold photoelectron photoion coincidence technique (TPEPICO) is used to define the energy initially deposited into the cluster ions. Metastable unimolecular decay (µs range) is studied using the RETOF's capacity for energy analysis. Under collision free conditions the by far most prominent metastable process is the evaporation of one neutral NH₃ monomer from protonated clusters (NH₃) _{n ? 2}NH ₄ ⁺ . Abundance of homogeneous vs. protonated cluster ions and of metastable fragments are reported as a function of photon energy and cluster size up ton=10.