A stereoselectively deuterated supramolecular motif to probe the role of solvent during self-assembly processes

S. Cantekin, Y. Nakano, J. C. Everts, P. van der Schoot, E. W. Meijer and A. R. A. Palmans

Chem. Commun., 2012, 48, 3803-3805

Small changes in the alkane solvent structure in combination with temperature effects lead to four different conformations of stereoselectively deuterated benzene-1,3,5-tricarboxamides in the aggregated state, affecting the expression of the supramolecular chirality and highlighting the role of the solvent structure in self-assembly processes.

Topological phase transitions driven by next-nearest-neighbor hopping in two-dimensional lattices

W. Beugeling, J. C. Everts and C. Morais Smith

Phys. Rev. B 2012, 86, 195129

For two-dimensional lattices in a tight-binding description, the intrinsic spin-orbit coupling, acting as a complex next-nearest-neighbor hopping, opens gaps that exhibit the quantum spin Hall effect. In this paper, we study the effect of a real next-nearest-neighbor hopping term on the band structure of several Dirac systems. In our model, the spin is conserved, which allows us to analyze the spin Chern numbers. We show that in the Lieb, kagome, and T3 lattices, variation of the amplitude of the real next-nearest-neighbor hopping term drives interesting topological phase transitions. These transitions may be experimentally realized in optical lattices under shaking, when the ratio between the nearest- and next-nearest-neighbor hopping parameters can be tuned to any possible value. Finally, we show that in the honeycomb lattice, next-nearest-neighbor hopping only drives topological phase transitions in the presence of a magnetic field, leading to the conjecture that these transitions can only occur in multigap systems.

Stable, ordered multilayers of partially fluorinated bolaamphiphiles at the air–water interface

J. Paczesny, P. Nitoń, A. Żywociński, K. Sozański, R. Hołyst, M. Fiałkowski, R. Kieffer, B. Glettner, C. Tschierske, D. Pociecha and E. Górecka

Soft Matter, 2012,8, 5262-5272

The article presents systematic research on Langmuir films of partially fluorinated bolaamphiphiles of different shapes. Such films exhibit a layering transition from a monolayer to a trilayer during compression on the air–water interface. Further compression gives different results depending on the shape and degree of fluorination of the molecules. Partially fluorinated compounds form well defined multilayers in a reversible process. The balance between rigidity and flexibility of the molecules, adjusted by the fluorination and shape of the molecules, seems to be the key factor in avoiding irreversible aggregation of the molecules and creating ordered multilayer structures. Anchor-shaped bolaamphiphiles form a trilayer and, subsequently, a 9-layer film due to a double roll-over mechanism. In contrast, when trilayer films of X-shaped bolaamphiphiles are compressed, 5- and 7-layer films are created according to a different mechanism. Films of thickness of up to nine layers were transferred from the water surface to solid substrates in a single step procedure without any distortion in the structure of the layers. X-ray reflectometry (XRR) was used to measure the thickness of the layers. Perfect fits of the XRR data to theoretical equations allowed for a conclusion that the multilayers are well-ordered lamellar structures. These investigations lead to an improvement in the general understanding of trilayer and multilayer formation and indicate that only in exceptional cases it happens due to a roll-over process.

Spontaneous self-assembly of partially fluorinated bolaamphiphiles into ordered layered structures

J. Paczesny, K. Sozański, A. Żywociński, R. Hołyst, B. Glettner, R. Kieffer, C. Tschierske, K. Nikiforov, D. Pociecha and E. Górecka

Phys. Chem. Chem. Phys., 2012, 14, 14365-14373

We developed a simple method for preparation of well-defined films of X-, T- and anchor-shaped bolaamphiphiles. The compounds were judiciously chosen to investigate the influence of the general molecular structure on the self-assembly properties. Precisely calculated (on the basis of Langmuir π(A) isotherms) volumes of chloroform solutions of the compounds of known concentrations were spread (drop-casted) directly onto the surface of water or silicon wafer. During the solvent evaporation, regular thin films were spontaneously formed. With use of the drop-casting (DC) method, films of thickness of up to three molecular layers could be obtained. X-ray reflectivity (XRR) measurements gave insight into arrangement of the molecules within the films. Different models of molecular organisation in the films were confronted with the experimental results. Advanced fitting procedures allowed for precise determination of the structure of the films. Comparison of films of different compounds obtained using different methods (Langmuir–Blodgett, DC) allowed for a deeper insight into the process of self-assembly, providing guidelines for designing functional molecules spontaneously forming thin, regular films. The proposed DC procedure is a novel alternative to broadly used self-assembled monolayers (SAMs). Unlike SAMs, our method does not require specific molecule–surface interactions and allows formation of films thicker than a monolayer.

The effect of depletion layer on diffusion of nanoparticles in solutions of flexible and polydisperse polymers

A. Ochab-Marcinek, S. A. Wieczorek, N. Ziębacza and R. Hołyst

Soft Matter, 2012, 8, 11173-11179

We introduce a model of diffusion of nanoparticles in solutions of flexible, polydisperse polymers. The model takes into account the effect of depletion layer with soft boundaries. The presence of depletion layer leads to nonlinear dependence of the mean square displacement (MSD) on time. Our model may be an alternative choice for the study of those experimental systems where the crossover between subdiffusion and normal diffusion is observed. Its advantage is mathematical simplicity: it allows easy identification of the crossover times and distances, which are here associated with the depletion layer thickness. The soft boundaries of the depletion layer, generated by the flexible and polydisperse polymers, are here approximated by two shells enclosed one in another, which may be interpreted as approximations of polymer density profiles around the probe. We show a very good agreement of the model with dynamic light scattering (DLS) measurements of diffusion of nanoparticles in solutions of polyethylene glycol (PEG).

Eu(III)-coupled luminescent multi-walled carbon nanotubes in surfactant solutions

X. Xina, M. Pietraszkiewicz, O. Pietraszkiewicz, O. Chernyayeva, T. Kalwarczyk, E. Gorecka, D. Pociecha, H. Li and R. Hołyst

Carbon 2012, 50, 2, 436-443

A carbon nanotube/inorganic hybrid material has been fabricated by coupling Eu(III) complexes onto multi-walled carbon nanotubes (MWCNTs). Successful coupling has been verified by X-ray photoelectron spectroscopy (XPS) measurement where a clear signal from Eu3d has been identified. When sonicated in hexaethylene glycol monododecyl ether (C12E6) or sodium dodecyl sulfate (SDS) aqueous solutions, the MWCNTs with Eu-complex attached (denoted as Eu-MWCNTs hereafter) can be dispersed. UV–vis measurements on a dilute dispersion of Eu-MWCNTs in SDS aqueous solution reveal the characteristic absorption from Eu(III) complexes, which gives further proof of the successful coupling. The strong luminescent properties of Eu-MWCNTs allow them to be observed directly under a fluorescence microscope. Interestingly, it is found that Eu-MWCNTs can undergo continuous movements in C12E6 or SDS dilute solutions. When Eu-MWCNTs are incorporated into the lvotropic liquid crystal phase formed by C12E6 (above 40% by weight), however, movements have been hindered. Small angle X-ray scattering measurements showed that Eu-MWCNTs are ordered in the lyotropic liquid crystal.  Fluorescence microscopy observations reveal that the luminescent properties of the Eu-MWCNTs have not been affected by the liquid crystalline surfactant matrix.

Autonomous Self‐Assembly of Ionic Nanoparticles into Hexagonally Close‐Packed Lattices at a Planar Oil–Water Interface

V. Sashuk, R. Hołyst, T. Wojciechowski, E. Górecka and M. Fiałkowski

Chemistry—A European Journal 2012, 18, 8, 2235-2238

Let’s get charged! Positively charged nanoparticles (NPs) spontaneously self‐assemble into hexagonally close‐packed lattices at a planar CH2Cl2–water interface (see figure). The self‐assembly process is fully autonomous and occurs without any external manipulation.

Formation of net-like patterns of gold nanoparticles in liquid crystal matrix at the air–water interface

J. Paczesny, K. Sozański, I. Dzięcielewski, A. Żywociński and R. Hołyst

Journal of Nanoparticle Research 2012, 14, Article number: 826

Controlled patterning and formation of nanostructures on surfaces based on self-assembly is a promising area in the field of “bottom-up” nanomaterial engineering. We report formation of net-like structures of gold nanoparticles (Au NPs) in a matrix of liquid crystalline amphiphile 4′-n-octyl-4-cyanobiphenyl at the air–water interface. After initial compression to at least 18 mN m−1, decompression of a Langmuir film of a mixture containing both components results in formation of net-like structures. The average size of a unit cell of the net is easily adjustable by changing the surface pressure during the decompression of the film. The net-like patterns of different, desired average unit cell areas were transferred onto solid substrates (Langmuir–Blodgett method) and investigated with scanning electron microscopy and X-ray reflectivity (XRR). Uniform coverage over large areas was proved. XRR data revealed lifting of the Au NPs from the surface during the formation of the film. A molecular mechanism of formation of the net-like structures is discussed.

Collapse of a nanoscopic void triggered by a spherically symmetric traveling sound wave

R. Hołyst, M. Litniewski and P. Garstecki

Phys. Rev. E 2012, 85, 056303

Molecular-dynamics simulations of the Lennard-Jones fluid (up to 107 atoms) are used to analyze the collapse of a nanoscopic bubble. The collapse is triggered by a traveling sound wave that forms a shock wave at the interface. The peak temperature Tmax in the focal point of the collapse is approximately ΣRa0, where Σ is the surface density of energy injected at the boundary of the container of radius R0 and α ≈ 0.4–0.45. For Σ = 1.6 J/m2 and R0 = 51 nm, the shock wave velocity, which is proportional toΣ, reaches 3400 m/s (4 times the speed of sound in the liquid); the pressure at the interface, which is proportional to Σ, reaches 10 GPa; and Tmax reaches 40 000 K. The Rayleigh-Plesset equation together with the time of the collapse can be used to estimate the pressure at the front of the shock wave.

Close-packed monolayers of charged Janus-type nanoparticles at the air–water interface

R. Hołyst, T. Wojciechowski and M. Fiałkowski

Journal of Colloid and Interface Science 2012, 375, 1, 180-186

We present a new method to obtain close-packed monolayers composed of noble metal nanoparticles (NP) possessing well-defined permanent charge of either sign. The method is based on the fact that ligands forming the protecting layer exhibit ability to rearrange at the NPs surface. We demonstrate that if the protecting layer is composed of a mixture of hydrophobic and hydrophilic charged ligands in appropriate proportion, the NP exhibits properties of a Janus-type particle with one of the hemispheres hydrophilic and the other hydrophobic. Such amphiphilic NPs self-assemble into a monolayer of well defined surface charge at the air–water interface. Due to strong stabilizing effect of the lateral electrostatic repulsions, such monolayer can be compressed to form close-packed hexagonal structure, and then easily transferred onto a solid substrate with the Langmuir–Blodgett technique.

Immobilization of galactose oxidase on self‐assembled monolayers of thiols on Au and Ag surfaces

A. Kaminska and R. Hołyst

Journal of Raman Spectroscopy 2012, 43, 7, 959-962

Galactose oxidase (GalOD) was immobilized on self‐assembled monolayers of thiols on silver and gold surfaces using trans‐stilbene (4,4′‐diisothiocyanate)‐2,2′disulphonic acid (DIDS) as the bridging compound. DIDS is the symmetrical bifunctional reagent that reacted with the amine moiety of the thiol and with primary amino groups of enzyme. The Raman measurement revealed that onto cysteamine‐modified silver and gold electrodes, bands corresponding to the galactose oxidase (about 694, 1076, 1274 cm—1 on Au and 762, 1058, 1274 cm–1 on Ag ) appeared and clearly demonstrated its immobilization onto Au and Ag surfaces. Simultaneously, we have also observed changes in the ratio of trans–gauche conformers of adsorbed cysteamine molecules. Layers revealing high content of trans conformer are transformed into layers composed mainly of cysteamine molecule in gauche conformation after galactose oxidase adsorption. These observations deliver a strong support for enzyme immobilization on cysteamine‐modified gold and silver surfaces. The surface plasmon resonance experiment gave a surface coverage of ~8.4 × 107 g/cm2 for gold electrode modified cysteamine using DIDS chemistry and 1.1 × 107 g/cm2 for the cysteamine only modified gold substrate and demonstrated that galactose oxidase layers immobilized with DIDS coupling reagent are quite stable and cannot be easily removed from the surface by treatment with a buffer solution. The surface plasmon resonance results indicated that in this method, a multilayer of galactose oxidase have been immobilized. Our new method of covalent attachment of enzymes seems to be quite promising as a new way of manufacturing biosensors. Copyright © 2012 John Wiley & Sons, Ltd.

Characterization of Caulobacter crescentus FtsZ Protein Using Dynamic Light Scattering

S. Hou, S. A. Wieczorek, T. S. Kaminski, N. Ziebacz, M. Tabaka, N. A. Sorto, M. H.Foss, J. T. Shaw, M. Thanbichler, D. B.Weibel, K. Nieznanski, R. Holyst and P. Garstecki

Journal of biological chemistry, Volume 287, Issue 28, 6 July 2012, Pages 23878-23886

The self-assembly of the tubulin homologue FtsZ at the mid-cell is a critical step in bacterial cell division. We introduce dynamic light scattering (DLS) spectroscopy as a new method to study the polymerization kinetics of FtsZ in solution. Analysis of the DLS data indicates that the FtsZ polymers are remarkably monodisperse in length, independent of the concentrations of GTP, GDP, and FtsZ monomers. Measurements of the diffusion coefficient of the polymers demonstrate that their length is remarkably stable until the free GTP is consumed. We estimated the mean size of the FtsZ polymers within this interval of stable length to be between 9 and 18 monomers. The rates of FtsZ polymerization and depolymerization are likely influenced by the concentration of GDP, as the repeated addition of GTP to FtsZ increased the rate of polymerization and slowed down depolymerization. Increasing the FtsZ concentration did not change the size of FtsZ polymers; however, it increased the rate of the depolymerization reaction by depleting free GTP. Using transmission electron microscopy we observed that FtsZ forms linear polymers in solutions which rapidly convert to large bundles upon contact with surfaces at time scales as short as several seconds. Finally, the best studied small molecule that binds to FtsZ, PC190723, had no stabilizing effect on Caulobacter crescentus FtsZ filaments in vitro, which complements previous studies with Escherichia coli FtsZ and confirms that this class of small molecules binds Gram-negative FtsZ weakly.

Three Steps of Hierarchical Self Assembly Toward a Stable and Efficient Surface Enhanced Raman Spectroscopy Platform

J. Paczesny, A. Kamińska, W. Adamkiewicz, K. Winkler, K. Sozanski, M. Wadowska, I. Dziecielewski and R. Holyst

Chem. Mater. 2012, 24, 19, 3667–3673

We report an innovative application of a true “bottom-up” approach for preparation of functional material. Three consecutive self-assembly steps were utilized for formation of a complex surface enhanced Raman spectroscopy (SERS) platform. First the Langmuir–Blodgett technique was used to deposit gold nanoparticles on a solid substrate. Thus prepared surfaces were afterward used as substrates in the chemical vapor deposition process of gallium nitride (GaN) nanowire growth. On such scaffolding, a third step of material fabrication was performed. Gold microflowers (Au MFs) deposited from solution preferably appeared at the top of the GaN nanowires and not in the cavities in between. The obtained morphology of the final material was controlled at each step of the preparation process to tailor its properties for desired purposes. Prepared surfaces were tested as SERS platforms. The enhancement factor was around 107 in case of p-mercaptobenzoic acid (p-MBA). The platforms were also suitable for biological and biomedical applications. We demonstrated the label free detection of DNA. The substrates gave reproducible SERS spectra both across a single platform and between different platforms. The average spectral correlation coefficients (Γ) was 0.87. Moreover, the obtained material proved to be very stable. The presented complex structure demonstrated therefore had the advantages of the two surface functionalization concepts it comprised: (1) GaN nanowire growth and (2) Au MF deposition, eliminating their major drawbacks. Presented material combined high SERS enhancement factor of Au MFs deposited on a flat surface and good durability of microflowers deposited on a surface completely covered with nanowires, which were almost SERS inactive. The final product provided truly exceptional stability and repeatability of SERS results, maintaining an enhancement factor comparable to the best commercially available platforms.

Electrodeposition of Well-Adhered Multifarious Au Particles at a Solid|Toluene|Aqueous Electrolyte Three-Phase Junction

I. Kaminska, M. Jonsson-Niedziolka, A. Kaminska, M. Pisarek, R. Hołyst, M. Opallo, and J. Niedziolka-Jonsson

J. Phys. Chem. C 2012, 116, 42, 22476–22485

In order to obtain uniform and reproducible surface enhanced Raman spectroscopy (SERS) platforms, a novel method for deposition of well-adhered multifarious gold particles on a tin-doped indium oxide electrode through electrogeneration at an electrode|gold compound in toluene|aqueous-electrolyte three-phase junction was developed. The electrodeposition was carried out both by double-potential-step chronoamperometry with one pulse for nucleation and one for growth of the particles, and by potentiostatic single-potential-step chronoamperometry. Both procedures give angular, multifarious Au particles with a diameter of 150 ± 40 nm. The size of the particles is independent of deposition time, after an initial growth phase, and controlled by the formation of a microemulsion at the three-phase junction. The particles are likely deposited from the microdroplets and their size is determined by the amount of gold salt in a droplet. The mechanism involves electoreduction of tetraoctylammonium tetrachloroaurate at the tin-doped indium oxide electrode followed by ion transfer across the liquid|liquid interface. The Au particles are strongly adhered to the electrode surface. The Au particle covered electrode enhances Raman scattering on the order of 105–106 times for malachite green isothiocyanate. Surface enhanced Raman spectroscopy studies reveal that the reproducibility of the Au particle deposit is excellent both between samples (<15% RSD) and across a single sample (<12% RSD). The obtained nanoparticulate deposit was also demonstrated to show electrocatalytic activity toward dioxygen reduction.

Biologistics-Diffusion coefficients for complete proteome of Escherichia coli

T. Kalwarczyk, M. Tabaka and R. Holyst

Bioinformatics, Volume 28, Issue 22, 15 November 2012, Pages 2971–2978

Motivation: Biologistics provides data for quantitative analysis of transport (diffusion) processes and their spatio-temporal correlations in cells. Mobility of proteins is one of the few parameters necessary to describe reaction rates for gene regulation. Although understanding of diffusion-limited biochemical reactions in vivo requires mobility data for the largest possible number of proteins in their native forms, currently, there is no database that would contain the complete information about the diffusion coefficients (DCs) of proteins in a given cell type.

Results: We demonstrate a method for the determination of in vivo DCs for any molecule—regardless of its molecular weight, size and structure—in any type of cell. We exemplify the method with the database of in vivo DC for all proteins (4302 records) from the proteome of K12 strain of Escherichia coli, together with examples of DC of amino acids, sugars, RNA and DNA. The database follows from the scale-dependent viscosity reference curve (sdVRC). Construction of sdVRC for prokaryotic or eukaryotic cell requires ~20 in vivo measurements using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), nuclear magnetic resonance (NMR) or particle tracking. The shape of the sdVRC would be different for each organism, but the mathematical form of the curve remains the same. The presented method has a high predictive power, as the measurements of DCs of several inert, properly chosen probes in a single cell type allows to determine the DCs of thousands of proteins. Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo.

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