Nanostructure and mechanics of mummified type I collagen from the 5300-year-old Tyrolean Iceman

Skin protects the body from pathogens and degradation. Mummified skin in particular is extremely resistant to decomposition. External influences or the action of micro-organisms, however, can degrade the connective tissue and lay the subjacent tissue open. To determine the degree of tissue preservation in mummified human skin and, in particular, the reason for its durability, we investigated the structural integrity of its main protein, type I collagen. We extracted samples from the Neolithic glacier mummy known as ‘the Iceman’. Atomic force microscopy (AFM) revealed collagen fibrils that had characteristic banding patterns of 69 ± 5 nm periodicity. Both the microstructure and the ultrastructure of dermal collagen bundles and fibrils were largely unaltered and extremely well preserved by the natural conservation process. Raman spectra of the ancient collagen indicated that there were no significant modifications in the molecular structure. However, AFM nanoindentation measurements showed slight changes in the mechanical behaviour of the fibrils. Young's modulus of single mummified fibrils was 4.1 ± 1.1 GPa, whereas the elasticity of recent collagen averages 3.2 ± 1.0 GPa. The excellent preservation of the collagen indicates that dehydration owing to freeze-drying of the collagen is the main process in mummification and that the influence of the degradation processes can be addressed, even after 5300 years

Initial coupling and reaction progression of directly deposited biradical graphene nanoribbon monomers on iodine-passivated versus pristine Ag(111)

The development of widely applicable methods for the synthesis of C-C-bonded nanostructures on inert and insulating surfaces is a challenging yet rewarding milestone in the field of on-surface synthesis. This would enable studies of nearly unperturbed covalent nanostructures with unique electronic properties as graphene nanoribbons (GNR) and π-conjugated 2D polymers. The prevalent Ullmann-type couplings are almost exclusively carried out on metal surfaces to lower the temperature required for initial dehalogenation well below the desorption threshold. To overcome the necessity for the activation of monomers on the target surface, we employ a recently developed Radical Deposition Source (RaDeS) for the direct deposition of radicals onto inert surfaces for subsequent coupling by addition reactions. The radicals are generated en route by indirect deposition of halogenated precursors through a heated reactive tube, where the dehalogenation reaction proceeds. Here, we use the ditopic 6,11-diiodo-1,2,3,4-tetraphenyltriphenylene (DITTP) precursor that afforded chevron-like GNR on Au(111) via the usual two-staged reaction comprised of monomer-coupling into covalent polymers and subsequent formation of an extended GNR by intramolecular cyclodehydrogenation (CDH). As a model system for inert surfaces, we use Ag(111) passivated with a closed monolayer of chemisorbed iodine that behaves in an inert manner with respect to dehalogenation reactions and facilitates the progressive coupling of radicals into extended covalent structures. We deposit the DITTP-derived biradicals onto both iodine-passivated and pristine Ag(111) surfaces. While on the passivated surface, we directly observe the formation of covalent polymers, on pristine Ag(111) organometallic intermediates emerge instead. This has decisive consequences for the further progression of the reaction: heating the organometallic chain directly on Ag(111) results in complete desorption, whereas the covalent polymer on iodine-passivated Ag(111) can be transformed into the GNR. Yet, the respective CDH proceeds directly on Ag(111) after thermal desorption of the iodine passivation. Accordingly, future work is aimed at the further development of approaches for the complete synthesis of GNR on inert surfaces

Competitive metal‐coordination of hexaaminotriphenylene on Cu(111) by intrinsic copper versus extrinsic nickel adatoms

The interplay between self‐assembly and surface chemistry of 2,3,6,7,10,11‐hexaminotriphenylene (HATP) on Cu(111) was complementarily studied by high‐resolution Scanning‐Tunneling‐Microscopy (STM) and X‐ray Photoelectron Spectroscopy (XPS) under ultra‐high vacuum conditions. To shed light on competitive metal‐coordination, comparative experiments were carried out on pristine and nickel‐covered Cu(111). Directly after room temperature deposition of HATP onto pristine Cu(111) self‐assembled aggregates were observed by STM, while XPS indicated non‐deprotonated amino groups. Annealing up to 200 °C activated the progressive single deprotonation of all amino groups as indicated by chemical shifts of both N 1s and C 1s core levels in the XP spectra. This enabled the formation of topologically versatile π‐d conjugated coordination networks with intrinsic copper adatoms. The basic motif of these networks was a metal‐organic trimer, where three HATP molecules were coordinated by Cu3 clusters, as corroborated by accompanying Density Functional Theory (DFT) simulations. Additional deposition of more reactive nickel atoms resulted in both chemical and structural changes with deprotonation and formation of bis(diimino)‐Ni bonded networks already at room temperature. Even though fused hexagonal pores were observed, extended honeycomb networks remained elusive, as tentatively explained by a restricted reversibility of these metal‐organic bonds

LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)

Background: Leucine-rich repeats (LRRs) are present in more than 6000 proteins. They are found in organisms ranging from viruses to eukaryotes and play an important role in protein-ligand interactions. To date, more than one hundred crystal structures of LRR containing proteins have been determined. This knowledge has increased our ability to use the crystal structures as templates to model LRR proteins with unknown structures. Since the individual three-dimensional LRR structures are not directly available from the established databases and since there are only a few detailed annotations for them, a conformational LRR database useful for homology modeling of LRR proteins is desirable. Description: We developed LRRML, a conformational database and an extensible markup language (XML) description of LRRs. The release 0.2 contains 1261 individual LRR structures, which were identified from 112 PDB structures and annotated manually. An XML structure was defined to exchange and store the LRRs. LRRML provides a source for homology modeling and structural analysis of LRR proteins. In order to demonstrate the capabilities of the database we modeled the mouse Toll-like receptor 3 (TLR3) by multiple templates homology modeling and compared the result with the crystal structure. Conclusion: LRRML is an information source for investigators involved in both theoretical and applied research on LRR proteins. It is available at http://zeus.krist.geo.uni-muenchen.de/similar to lrrml

Mechanistic insights into on-surface reactions from isothermal temperature-programmed X-ray photoelectron spectroscopy

On-surface synthesis often proceeds under kinetic control due to the irreversibility of key reaction steps, rendering kinetic studies pivotal. The accurate quantification of reaction rates also bears potential for unveiling reaction mechanisms. Temperature-Programmed X-ray Photoelectron Spectroscopy (TP-XPS) has emerged as an analytical tool for kinetic studies with splendid chemical and sufficient temporal resolution. Here, we demonstrate that the common linear temperature ramps lead to fitting ambiguities. Moreover, pinpointing the reaction order remains intricate, although this key parameter entails information on atomistic mechanisms. Yet, TP-XPS experiments with a stepped temperature profile comprised of isothermal segments facilitate the direct quantification of rate constants from fitting time courses. Thereby, rate constants are obtained for a series of temperatures, which allows independent extraction of both activation energies and pre-exponentials from Arrhenius plots. By using two analogous doubly versus triply brominated aromatic model compounds, we found that their debromination on Ag(111) is best modeled by second-order kinetics and thus proceeds via the involvement of a second, non-obvious reactant. Accordingly, we propose that debromination is activated by surface supplied Ag adatoms. This hypothesis is supported by Density Functional Theory (DFT) calculations. We foresee auspicious prospects for this TP-XPS variant for further exploring the kinetics and mechanisms of on-surface reactions

Instabilities and disorder of the domain patterns in the systems with competing interactions

The dynamics of the domains is studied in a two-dimensional model of the microphase separation of diblock copolymers in the vicinity of the transition. A criterion for the validity of the mean field theory is derived. It is shown that at certain temperatures the ordered hexagonal pattern becomes unstable with respect to the two types of instabilities: the radially-nonsymmetric distortions of the domains and the repumping of the order parameter between the neighbors. Both these instabilities may lead to the transformation of the regular hexagonal pattern into a disordered pattern.Comment: ReVTeX, 4 pages, 3 figures (postscript); submitted to Phys. Rev. Let

A Phase-Field Model of Spiral Dendritic Growth

Domains of condensed-phase monolayers of chiral molecules exhibit a variety of interesting nonequilibrium structures when formed via pressurization. To model these domain patterns, we add a complex field describing the tilt degree of freedom to an (anisotropic) complex-phase-field solidification model. The resulting formalism allows for the inclusion of (in general, non-reflection symmetric) interactions between the tilt, the solid-liquid interface, and the bond orientation. Simulations demonstrate the ability of the model to exhibit spiral dendritic growth.Comment: text plus Four postscript figure file

Mid-infrared interference coatings with excess optical loss below 10 ppm

Low excess optical loss, combined absorption and scatter loss, is a key performance metric for any high-reflectance coating technology and is currently one of the main limiting factors for the application of optical resonators in the mid-infrared spectral region. Here we present high-reflectivity substrate-transferred single-crystal GaAs/AlGaAs interference coatings at a center wavelength of 4.54 µm with record-low excess optical loss below 10 parts per million. These high-performance mirrors are realized via a novel microfabrication process that differs significantly from the production of amorphous multilayers generated via physical vapor deposition processes. This new process enables reduced scatter loss due to the low surface and interfacial roughness, while low background doping in epitaxial growth ensures strongly reduced absorption. We report on a suite of optical measurements, including cavity ring-down, transmittance spectroscopy, and direct absorption tests to reveal the optical losses for a set of prototype mirrors. In the course of these measurements, we observe a unique polarization-orientation-dependent loss mechanism which we attribute to elastic anisotropy of these strained epitaxial multilayers. A future increase in layer count and a corresponding reduction of transmittance will enable optical resonators with a finesse in excess of 100,000 in the mid-infrared spectral region, allowing for advances in high-resolution spectroscopy, narrow-linewidth laser stabilization, and ultrasensitive measurements of various light–matter interactions

Thermodynamics of 4,4 '-stilbenedicarboxylic acid monolayer self-assembly at the nonanoic acid-graphite interface

A direct calorimetric measurement of the overall enthalpy change associated with self-assembly of organic monolayers at the liquid–solid interface is for most systems of interest practically impossible. In previous work we proposed an adapted Born–Haber cycle for an indirect assessment of the overall enthalpy change by using terephthalic acid monolayers at the nonanoic acid–graphite interface as a model system. To this end, the sublimation enthalpy, dissolution enthalpy, the monolayer binding enthalpy in vacuum, and a dewetting enthalpy are combined to yield the total enthalpy change. In the present study the Born–Haber cycle is applied to 4,40 -stilbenedicarboxylic acid monolayers. A detailed comparison of these two aromatic dicarboxylic acids is used to evaluate and quantify the contribution of the organic backbone for stabilization of the monolayer at the nonanoic acid–graphite interface