Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Carbohydrate Self-Assembly at Surfaces: STM Imaging of Sucrose Conformation and Ordering on Cu(100).

ABSTRACT: Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self-assembly of the disaccharide sucrose on a Cu(100) surface with subunit-level imaging. By employing a multistage modeling approach in combination with the experimental data, we can rationalize the conformation on the surface as well as the interactions between the sucrose molecules, thereby yielding models of the observed self-assembled patterns on the surface.

SUBMITTER: Abb S

PROVIDER: S-EPMC6771801 | biostudies-other | 2019 Apr

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Carbohydrate Self-Assembly at Surfaces: STM Imaging of Sucrose Conformation and Ordering on Cu(100).

Abb Sabine S Tarrat Nathalie N Cortés Juan J Andriyevsky Bohdan B Harnau Ludger L Schön J Christian JC Rauschenbach Stephan S Kern Klaus K

Angewandte Chemie (International ed. in English) 20190524 25

Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self-assembly of the disaccharide sucrose on a Cu(100) surface with subunit-level imaging. By employing a multistage modeling approach in combination with the experimental data, we can rationalize the conformation on the surface as well as the interacti ...[more]

PMID: 31018027

Similar Datasets

Self-assembly directed one-step synthesis of [4]radialene on Cu(100) surfaces.

Project description:The synthetic challenges of radialenes have precluded their practical applications. Here, we report a one-step synthetic protocol of [4]radialene on a copper surface. High-resolution scanning tunneling microscopy measurements reveal that such catalytic reaction proceeds readily with high selectivity at the temperature below 120 K. First-principles calculations show that the reaction pathway is characterized by firstly the cooperative inter-molecular hydrogen tautomerization and then the C-C bond formation. The feasibility of such cyclotetramerization reaction can be interpreted by the surface effect of Cu(100), which firstly plays an important role in directing the molecular assembly and then serves as an active catalyst in the hydrogen tautomerization and C-C coupling processes. This work presents not only a novel strategy to the scant number of synthetic methods to produce [4]radialenes via a novel [1 + 1 + 1 + 1] reaction pathway, but also a successful example of C-C bond coupling reactions guided by the surface-induced C-H/π assembly.

| S-EPMC6078953 | biostudies-literature

Mechanism Investigations on Water Gas Shift Reaction over Cu(111), Cu(100), and Cu(211) Surfaces.

Project description:Cu-based catalysts are commonly applied in low-temperature water gas shift (WGS) reactions, owing to their low cost and high catalytic activity. The influence of different Cu surfaces on catalytic activity and mechanism over the WGS reaction remains unclear. In this work, the effect of different structures of surfaces on the WGS mechanism is studied using density functional theory (DFT). Three surface terminations (Cu(100), Cu(111), and Cu(211)) of Cu are considered, and the coordination number (CN) of the active Cu site is in the range from 7 to 9. The most stable surface is Cu(211). Then, d-band center values are calculated, which decrease in the following sequence: Cu(211) > Cu(100) > Cu(111). This shows that d-band center values decrease with increasing coordination number. The increase in the centers of the d-band leads to an increase in the adsorption strength of CO and H2O adsorbates, which is in line with the theory of the d-band center. In addition, the further calculated mechanism for WGS reaction over three different Cu surfaces illustrates that the carboxyl path is the most favorable mechanism, and the rate-determining step is H2O dissociation. Cu(211) shows excellent WGS catalytic performance, better than the Cu(100) and Cu(111) surfaces. This work provides theoretical insights into the rational design of highly active Cu-based catalysts toward WGS reaction.

| S-EPMC8811938 | biostudies-literature

Self-assembly of graphene on carbon nanotube surfaces.

Project description:The rolling up of a graphene sheet into a tube is a standard visualization tool for illustrating carbon nanotube (CNT) formation. However, the actual processes of rolling up graphene sheets into CNTs in laboratory syntheses have never been demonstrated. Here we report conformal growth of graphene by carbon self-assembly on single-wall and multi-wall CNTs using chemical vapor deposition (CVD) of methane without the presence of metal catalysts. The new graphene layers roll up into seamless coaxial cylinders encapsulating the existing CNTs, but their adhesion to the primary CNTs is weak due to the existence of lattice misorientation. Our study shows that graphene nucleation and growth by self-assembly of carbon on the inactive carbon basal plane of CNTs occurs by a new mechanism that is markedly different from epitaxial growth on metal surfaces, opening up the possibility of graphene growth on many other non-metal substrates by simple methane CVD.

| S-EPMC3733056 | biostudies-literature

Self-assembly of facially amphiphilic dendrimers on surfaces.

Project description:Facially amphiphilic dendrimers have been shown to provide significant difference in surface behavior due to subtle changes in structure. The monodendrons are capable of providing hydrophobic surfaces, while the didendrons provide superhydrophobic surfaces. This provides an example of how a molecular level change could result in significant changes in surface behavior. This difference is attributed to the conformational differences exhibited by these dendrimers on surfaces.

| S-EPMC2518940 | biostudies-literature

Self-assembly of convex particles on spherocylindrical surfaces.

Project description:The precise control of assembly and packing of proteins and colloids on curved surfaces has fundamental implications in nanotechnology. In this paper, we describe dynamical simulations of the self-assembly of conical subunits around a spherocylindrical template, and a continuum theory for the bending energy of a triangular lattice with spontaneous curvature on a surface with arbitrary curvature. We find that assembly depends sensitively on mismatches between subunit spontaneous curvature and the mean curvature of the template, as well as anisotropic curvature of the template (mismatch between the two principal curvatures). Our simulations predict assembly morphologies that closely resemble those observed in experiments in which virus capsid proteins self-assemble around metal nanorods. Below a threshold curvature mismatch, our simulations identify a regime of optimal assembly leading to complete, symmetrical particles. Outside of this regime we observe defective particles, whose morphologies depend on the degree of curvature mismatch. To learn how assembly is affected by the nonuniform curvature of a spherocylinder, we also study the simpler cases of assembly around spherical and cylindrical cores. Our results show that both the intrinsic (Gaussian) and extrinsic (mean) curvatures of a template play significant roles in guiding the assembly of anisotropic subunits, providing a rich design space for the formation of nanoscale materials.

| S-EPMC6051892 | biostudies-literature

Amyloid Peptide Mixtures: Self-Assembly, Hydrogelation, Nematic Ordering, and Catalysts in Aldol Reactions.

Project description:Morphological, spectroscopic, and scattering studies of the self-assembly and aggregation of mixtures of [RF]4 and P[RF]4 peptides (where R = arginine; F = phenylalanine; P = proline), in solution and as hydrogels, were performed to obtain information about polymorphism. CD data confirmed a ?-sheet secondary structure in aqueous solution, and TEM images revealed nanofibers with diameters of ?10 nm and micrometer lengths. SAXS curves were fitted using a mass fractal-component and a long cylinder shell form factor for the liquid samples, and only a long cylinder shell form factor for the gels. Increasing the P[RF]4 content in the systems leads to a reduction in cylinder radius and core scattering density, suggesting an increase in packing of the peptide molecules; however, the opposite effect is observed for the gels, where the scattering density is higher in the shell for the systems containing higher P[RF]4 content. These compounds show potential as catalysts in the asymmetric aldol reactions, with cyclohexanone and p-nitrobenzaldehyde in aqueous media. A moderate conversion (36.9%) and a good stereoselectivity (69:31) were observed for the system containing only [RF]4. With increasing P[RF]4 content, a considerable decrease of the conversion was observed, suggesting differences in the self-assembly and packing factor. Rheological measurements were performed to determine the shear moduli for the soft gels.

| S-EPMC7146849 | biostudies-literature

Transferring Micellar Changes to Bulk Properties via Tunable Self-Assembly and Hierarchical Ordering.

Project description:Hierarchical self-assembly is an effective means of preparing useful materials. However, control over assembly across length scales is a difficult challenge, often confounded by the perceived need to redesign the molecular building blocks when new material properties are needed. Here, we show that we can treat a simple dipeptide building block as a polyelectrolyte and use polymer physics approaches to explain the self-assembly over a wide concentration range. This allows us to determine how entangled the system is and therefore how it might be best processed, enabling us to prepare interesting analogues to threads and webs, as well as films that lose order on heating and "noodles" which change dimensions on heating, showing that we can transfer micellar-level changes to bulk properties all from a single building block.

| S-EPMC9798853 | biostudies-literature

Plasma-assisted oxidation of Cu(100) and Cu(111).

Project description:Oxidized copper surfaces have attracted significant attention in recent years due to their unique catalytic properties, including their enhanced hydrocarbon selectivity during the electrochemical reduction of CO2. Although oxygen plasma has been used to create highly active copper oxide electrodes for CO2RR, how such treatment alters the copper surface is still poorly understood. Here, we study the oxidation of Cu(100) and Cu(111) surfaces by sequential exposure to a low-pressure oxygen plasma at room temperature. We used scanning tunnelling microscopy (STM), low energy electron microscopy (LEEM), X-ray photoelectron spectroscopy (XPS), near edge X-ray absorption fine structure spectroscopy (NEXAFS) and low energy electron diffraction (LEED) for the comprehensive characterization of the resulting oxide films. O2-plasma exposure initially induces the growth of 3-dimensional oxide islands surrounded by an O-covered Cu surface. With ongoing plasma exposure, the islands coalesce and form a closed oxide film. Utilizing spectroscopy, we traced the evolution of metallic Cu, Cu2O and CuO species upon oxygen plasma exposure and found a dependence of the surface structure and chemical state on the substrate's orientation. On Cu(100) the oxide islands grow with a lower rate than on the (111) surface. Furthermore, while on Cu(100) only Cu2O is formed during the initial growth phase, both Cu2O and CuO species are simultaneously generated on Cu(111). Finally, prolonged oxygen plasma exposure results in a sandwiched film structure with CuO at the surface and Cu2O at the interface to the metallic support. A stable CuO(111) surface orientation is identified in both cases, aligned to the Cu(111) support, but with two coexisting rotational domains on Cu(100). These findings illustrate the possibility of tailoring the oxidation state, structure and morphology of metallic surfaces for a wide range of applications through oxygen plasma treatments.

| S-EPMC8565394 | biostudies-literature

Just add sugar for carbohydrate induced self-assembly of curcumin.

Project description:In nature, self-assembly processes based on amphiphilic molecules play an integral part in the design of structures of higher order such as cells. Among them, amphiphilic glycoproteins or glycolipids take on a pivotal role due to their bioactivity. Here we show that sugars, in particular, fructose, are capable of directing the self-assembly of highly insoluble curcumin resulting in the formation of well-defined capsules based on non-covalent forces. Simply by mixing an aqueous solution of fructose and curcumin in an open vessel leads to the generation of capsules with sizes ranging between 100 and 150?nm independent of the initial concentrations used. Our results demonstrate that hydrogen bonding displayed by fructose can induce the self-assembly of hydrophobic molecules such as curcumin into well-ordered structures, and serving as a simple and virtually instantaneous way of making nanoparticles from curcumin in water with the potential for template polymerization and nanocarriers.

| S-EPMC6362107 | biostudies-literature

Magnetic self-assembly of three-dimensional surfaces from planar sheets.

Project description:This report describes the spontaneous folding of flat elastomeric sheets, patterned with magnetic dipoles, into free-standing, 3D objects that are the topological equivalents of spherical shells. The path of the self-assembly is determined by a competition between mechanical and magnetic interactions. The potential of this strategy for the fabrication of 3D electronic devices is demonstrated by generating a simple electrical circuit surrounding a spherical cavity.

| S-EPMC554830 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data