Showing papers by "Fritz Haber Institute of the Max Planck Society published in 1993"

The portal protein of bacteriophage SPP1: a DNA pump with 13-fold symmetry.

Abstract: Electron microscopy in combination with image processing is a powerful method for obtaining structural information on non-crystallized biological macromolecules at the 10-50 A resolution level. The processing of noisy microscopical images requires advanced data processing methodologies in which one must carefully avoid the introduction of any form of bias into the data set. Using a novel multivariate statistical approach to the analysis of symmetry, we studied the structure of the bacteriophage SPP1 portal protein oligomer. This portal structure, ubiquitous in icosahedral bacteriophages which package dsDNA, is located at the site of symmetry mismatch between a 5-fold vertex of the icosahedral shell and the 6-fold symmetric (helical) tail. From previous studies such 'head-to-tail connector' structures were generally accepted to be homododecamers assembled in a 12-fold symmetric ring around a central channel. Using a new analysis methodology we have found that the phage SPP1 portal structure exhibits 13-fold cyclical symmetry: a new point group organization for oligomeric proteins. A model for the DNA packaging mechanism by 13-fold symmetric portal protein assemblies is presented which attributes a coherent functional meaning to their unusual symmetry.

Etching of Silicon in NaOH Solutions II . Electrochemical Studies of n‐Si(111) and (100) and Mechanism of the Dissolution

Abstract: In Part I of this work, the bias dependence of the etching of silicon (111) has been investigated by means of in situscanning tunneling microscopy observations. In this second part, current‐voltage curves and etch rate results derived from the loss of material and performed with n‐type Si samples of various orientations, show that electrochemical and chemical reactions coexist in the oxidation of Si. A model is presented for the oxidation of a Si atom in a kink site in different situations of polarization. The key feature of the description is the understanding of the persistent hydrogen termination of the surface in spite of the continuous oxidative removal of Si atoms from the surface. The model includes the hydrolytic splitting of Si—H and Si—Si bonds as the important chemical contributions to the etching process. At the rest potential, the chemical component is dominant. The sequence of reactions leaves the surface in the terminated state. The anodic current is due to the injection of electrons which are produced during the substitution of Si—H by Si—OH bonds. This results above a critical electrode potential in passivation. In this respect, (111) and (100) faces present quite different behaviors. At cathodic bias where the hydrogen evolution becomes fast, due to the accumulation of electrons at the surface, not only the anodic component of the etching reaction vanishes but also the chemical component decreases in rate and is eventually stopped.

K-shell excitation of the water, ammonia, and methane molecules using high-resolution photoabsorption spectroscopy.

Abstract: The K-shell excitation spectra of the hydrides water, ammonia, and methane have been measured in photoabsorption experiments using synchrotron radiation in combination with a high-resolution monochromator. For the case of methane, in particular, a wealth of spectral detail is observed which was not accessible in previous studies. The measured excitation energies and relative intensities compare well with values calculated using a complete second-order approximation for the polarization propagator. In order to determine the extent of admixing of valence excitations (i.e., transitions into virtual ${\mathrm{\ensuremath{\sigma}}}^{\mathrm{*}}$ orbitals) to the Rydberg manifolds, the X-H bond lengths have been varied in the calculations. In the case of ${\mathrm{H}}_{2}$O, the two lowest-energy bands are due to the O 1s-4${\mathit{a}}_{1}$/3s and O 1s-2${\mathit{b}}_{2}$/3p transitions and have strong valence character; their width indicates that both excitations are dissociative. The ${\mathrm{NH}}_{3}$ and ${\mathrm{ND}}_{3}$ spectra are also broad which is not only due to possible dissociation but also to unresolved vibrational fine structure (${\ensuremath{ u}}_{2}$ mode) and a Jahn-Teller instability. Valence character is concentrated in the lowest excited state in the Rydberg ns manifold, but is distributed more uniformly over the np(e) manifold. The weak dipole-forbidden C 1s-3s(${\mathit{a}}_{1}$) transition in ${\mathrm{CH}}_{4}$ and ${\mathrm{CD}}_{4}$ is accompanied by vibrational structure due to the ${\ensuremath{ u}}_{4}$ mode, indicating that it derives its intensity from vibronic coupling with the C 1s-3p(${\mathit{t}}_{2}$) transition. The structure on the latter band is extremely complicated due to Jahn-Teller coupling and cannot be assigned at present, as is the case for the Rydberg transitions at higher energies. The higher np Rydberg excitations contain considerable valence character.

Turbulence due to spiral breakup in a continuous excitable medium.

Abstract: Excitable media are extended spatial systems, which support the propagation of waves including pulses and rotating spirals. They are well described by sets of partial differential equations involving a fast activator and a slow inhibitor variable. Here we show that spiral breakup, leading to turbulence, can occur in a two-dimensional reaction-diffusion system with delayed-inhibitor production. Upon a decrease of excitability, spirals become unstable because their wavelengths and periods are too short to be sustained in the system.

On the nature of the active state of silver during catalytic oxidation of methanol

Abstract: Under the applied high reaction temperatures (∼900 K) the Ag surface is restructured and a tightly held oxygen species is formed on the surface (Oγ) apart from O atoms dissolved in the bulk (Oβ). Methanol oxidation to formaldehyde proceeds through this Oγ species as demonstrated by application of a variety of spectroscopic techniques.

Elastic constants of Cu and the instability of its bcc structure.

Abstract: First-principles full potential nonrelativistic calculations of the total energy of fcc Cu for various deformations of the cubic unit cell give values of the three elastic constants of fcc Cu in good agreement with experiment. Use is made of simple formulas for the strain energy of tetragonal and trigonal deformations in terms of the elastic constants. The total energy of Cu as a function of the shape of a body-centered-tetragonal cell at constant volume does not have a minimum at the bcc structure, and it is concluded that bcc Cu is unstable with respect to [110] shears. However, this instability does not prevent expitaxial growth on (001) surfaces.

The Mechanism of the Anodic Oxidation of Silicon in Acidic Fluoride Solutions Revisited

Abstract: The present experience of the electrochemical dissolution of silicon and previous assumptions upon the mechanism are briefly reviewed. A new model is developed which explains how the coverage of the surface by hydrogen can be maintained in spite of the continuous anodic dissolution.

Threefold-coordinated hollow adsorption site for Ni(111)-c(4 x 2)-CO: A surface-extended x-ray-absorption fine-structure study.

Abstract: Surface-extended x-ray-absorption fine-structure studies on the Ni(111)-c(4\ifmmode\times\else\texttimes\fi{}2)-CO system show that CO adsorbs in threefold-coordinated hollow sites. This result is in conflict with the adsorption-site determination via molecular vibrational frequencies, which for this system led to an assignment of a bridge site.

The formation of subsurface oxygen on Pt(100)

Abstract: PhotoEmission Electron Microscopy (PEEM) enables imaging a surface via its work function. If a CO covered Pt(100) surface is exposed to oxygen patches are formed which appear dark in the PEEM image due to their high work function. As the surface is heated to temperatures above 650 K we observe the conversion of these dark islands into very bright ones with work functions much lower than even that of the clean surface. These findings are attributed to a change in the dipole moment of the adsorbed oxygen induced by their migration beneath the surface. A total work-function decrease of up to 1.2 eV has been evaluated independently using a Scanning Photoemission Microscope (SPM). The properties of this new kind of oxygen were also further investigated with thermal desorption spectroscopy and with Auger-electron spectroscopy.

Model identification of a spatiotemporally varying catalytic reaction

Abstract: The occurrence of instabilities in chemically reacting systems, resulting in unsteady and spatially inhomogeneous reaction rates, is a widespread phenomenon. In this article, we use nonlinear signal processing techniques to extract a simple, but accurate, dynamic model from experimental data of a system with spatiotemporal variations. The approach consists of a combination of two steps. The proper orthogonal decomposition [POD or Karhunen-Loeve (KL) expansion] allows us to determine active degrees of freedom (important spatial structures) of the system. Projection onto these “modes” reduces the data to a small number of time series. Processing these time series through an artificial neural network (ANN) results in a low-dimensional, nonlinear dynamic model with almost quantitative predictive capabilities. This approach is demonstrated using spatiotemporal data from CO oxidation on a Pt (110) crystal surface. In this special case, the dynamics of the two-dimensional reaction profile can be successfully described by four modes; the ANN-based model not only correctly predicts the spatiotemporal short-term behavior, but also accurately captures the long-term dynamics (the attractor). While this approach does not substitute for fundamental modeling, it provides a systematic framework for processing experimental data from a wide variety of spatiotemporally varying reaction engineering processes.

Imaging the oscillating CO-oxidation on Pt-surfaces with field ion microscopy

Abstract: The oxidation of carbon monoxide on platinum surfaces is investigated by field ion microscopy (FIM) and compared to earlier work by field electron microscopy (FEM). The reaction gas is used as the field ion imaging gas at pressures of < 10−4 mbar and at temperatures of the catalytic reaction. In FIM the surface is imaged by O2+-ions which are preferentially ionized at oxygen-covered surface areas. During temperature variations regions of bistability could be detected by FEM and FIM. Finally self-sustained isothermal oscillations of the catalytic CO-oxidation could be measured from the periodic fluctuations of the O2+-field ion current. Atomic resolution shows that the Pt-(331) planes are the pace makers of the oscillation.

Global coupling in the presence of defects: Synchronization in an oscillatory surface reaction

Abstract: The transition from a spatially uniformly oscillating surface to the formation of chemical wave patterns has been investigated in the NO+CO reaction on Pt(100) using photoemission electron microscopy. This transition is associated with a discontinuous jump in the local oscillation frequency and can be described as a breakdown of global coupling caused by the presence of defects in the oscillating medium.

O- escape during the oxidation of cesium.

Abstract: Exposure of Cs surfaces to ${\mathrm{O}}_{2}$ causes ejection of ${\mathrm{O}}^{\mathrm{\ensuremath{-}}}$ ions with low yields (\ensuremath{\sim}${10}^{\mathrm{\ensuremath{-}}8}$ per incident ${\mathrm{O}}_{2}$ molecule) during the first stages of dissociative chemisorption (followed by exoelectron emission at higher exposures), although the work function of the surface exceeds the electron affinity of O and the energetics of the overall reaction is almost zero. A mechanism is proposed whereafter the release of ${\mathrm{O}}^{\mathrm{\ensuremath{-}}}$ is a consequence of strong repulsion in ${\mathrm{O}}_{2}^{2\mathrm{\ensuremath{-}}}$ species intermediately formed in front of the surface.

Ab-Initio Molecular Dynamics in the Full-Potential LMTO Method:. Derivation of a Practical Force Theorem

Abstract: A major advance in electronic structure calculations was the combination of local-density techniques with molecular dynamics by Car and Parrinello seven years ago. Unfortunately, application of the Car-Parrinello scheme has been limited essentially to sp materials because only in the plane-wave pseudopotential method forces are trivial to calculate. We present a systematic approach to derive force theorems with desired characteristics within complicated basis sets, which are applicable to all elements of the periodic table equally well. Application to the LMTO basis set yields an accurate force theorem, quite distinct from the Hellman-Feynman form, which is exceptionally insensitive to errors in the trial density. The forces were implemented in a new full-potential LMTO method which is suited to arbitrary geometries. First results for ab-initio molecular dynamics and simulated annealing runs are shown for some random small molecules and small clusters of silver atoms.

L2,3 edges of tetrahedrally coordinated d0 transition-metal oxyanions XO4n-

Abstract: The L2,3 edges of compounds containing tetrahedrally coordinated, isoelectronic d0 transition-metal oxyanions, TiO44-, VO43-, CrO42- and MnO4- have been measured using electron energy-loss spectroscopy (EELS). The general shape of the electron energy-loss near-edge fine structure (ELNES) is found to be remarkably similar for these oxyanions and arises from the atomic multiplet spectrum of the d0 transition-metal ion modified by the tetrahedral field due to the oxygen ligands. The observed structure is also discussed within the framework of molecular-orbital (MO) theory. The possibilities of using these spectra as fingerprints for d0 transition-metal ions in tetrahedral coordination is discussed. The structure observed at the O K edges is also commented upon in the light of these findings.

Electronic structure and bonding in the metallocarbohedrene Ti8C12.

Abstract: Total-energy and electronic-structure calculations are presented for a recently proposed dodecahedral cluster of eight titanium and twelve carbon atoms. The calculations were done using density-functional theory and a recently developed cluster full-potential linear muffin-tin orbital method which is suited to arbitrary geometries and permits direct evaluation of the forces. As in the ${\mathrm{C}}_{60}$ molecule, the atoms form a spherical grahitelike shell with a threefold coordination at all sites. The C-C and Ti-C bond lenghts are calculated to be of 2.63 and 3.76 bohrs, respectively, and the binding energy is 6.6 eV per atom. The bonding mechanism is quite different from that which stabilizes the graphite crystal or the ${\mathrm{C}}_{60}$ molecule.

Hubbard correlations and charge transfer at the GaAs(110) surface with alkali adsorbates.

Abstract: We have performed density-functional-theory (DFT) calculations for potassium adsorbed on GaAs(110). The results show that alkali adatoms mainly act as donors giving their electrons to Ga-derived surface states. We found that these states consist of well localized Ga dangling bonds, which allowed us to map the DFT results on a two-dimensional Hubbard model. To calculate the Hubbard U and the charge-transfer parameter \ensuremath{\Delta} we simulate the electron transfer between adjacent orbitals. We find that U and \ensuremath{\Delta} are of the same order as the hopping integral t, which brings the surface in the Mott-Hubbard regime.

Observation of nonisotropic Auger angular distribution in the C(1s) shape resonance of CO.

Abstract: Angle-resolved high-resolution C(KVV) Auger spectra of CO were taken in the vicinity of the C(1s) ${\mathrm{\ensuremath{\sigma}}}^{\mathrm{*}}$ shape resonance. These spectra show clear evidence for the theoretically predicted anisotropic K-shell Auger emission in molecules. Complementary results from angle-resolved photoion spectroscopy show that the small size of the observed effect is, besides the varying intrinsic anisotropy of the Auger decay, also due to a smaller anisotropy in the primary absorption process than originally predicted but in good agreement with more recent calculations. Contrary to this, satellite Auger transitions show unexpectedly large anisotropies.