From Random Coil to Extended Nanocylinder: Dendrimer Fragments Shape Polymer Chains

Wedgelike dendrimer fragments , “dendrons”, attached to linear polymers as side groups, can be used to create anisotropic “nanocylinders”, leading to uncoiling and extension of the polymer chains. Synthetic macromolecules of this type can be visualized directly on surfaces and their contour length determined from scanning force micrographs. Unexpected acceleration effects in the polymerization of dendron monomers as well as the structural consequences of dendritic “pieces of cake” (shown schematically) on linear polymer chains are discussed.     

Coalescence of polystyrene nodules in soft poly(butyl acrylate)-based films

A two-stage emulsion polymerization procedure was used in order to obtain core–shell polymer particles having a core of polystyrene (PS), covered by a shell of either pure poly(butyl acrylate) (PBA) or a methacrylic acid-functionalized PBA. Films were then cast from these latexes, and their properties were studied without further treatments (“as-dried” films), as well as after a 3 hr heat treatment intended to provoke the coalescence of PS domains (“annealed” films). “As-dried” and “annealed” film samples were studied by dynamic mechanical analysis (DMA), scanning electron microscopy (SEM) and small angle neutron scattering (SANS). DMA and SEM results, as described in previous works, showed that for unfunctionalized films, the percolated PS domains coalesced under the annealing treatment, while for the functionalized films, they did not. On the other hand, SANS results presented here showed that even in the case of functionalized films, the presence of coalescence could be detected. It was concluded that while DMA and SEM reveal large-scale modifications provoked by the heat treatment, SANS is capable of detecting very smallscale changes which do not have a direct effect on the bulk physical properties of the samples.     

Structural defects in periodic and quasicrystalline binary nanocrystal superlattices

Binary nanocrystal superlattices (BNSLs) emerge as an important class of man-made materials where components and functionalities can be added, tuned, or combined in a predictable manner. These amazingly complex structures spontaneously self-assemble from colloidal solutions containing binary mixtures of functional (semiconducting, magnetic, plasmonic, etc.) nanocrystals. Further developments of the BNSL-based materials require a deep understanding and control over BNSL formation and structural perfection. Like any solid, BNSL can contain different kinds of structural defects. It is well-known that defects can have a tremendous effect on the material's behavior. Defect engineering is used to modify and improve many of the mechanical, electrical, magnetic, and optical properties of conventional solids. In this work, we provide the first systematic analysis of structural defects in various BNSL structures. We used BNSLs as a platform for studying structural defects in both periodic (crystalline) and aperiodic (quasicrystalline) lattices, as well as for direct imaging of the interfaces between crystalline and quasicrystalline domains. Such direct observation of local imperfections in complex multicomponent lattices provides a unique insight into the fundamental aspects of crystal formation.     

Polyoxometalate-Engineered Building Blocks with Gold Cores for the Self-Assembly of Responsive Water-Soluble Nanostructures

The controlled assembly of gold nanoparticles (AuNPs) with the size of quantum dots into predictable structures is extremely challenging as it requires the quantitatively and topologically precise placement of anisotropic domains on their small, approximately spherical surfaces. We herein address this problem by using polyoxometalate leaving groups to transform 2 nm diameter gold cores into reactive building blocks with hydrophilic and hydrophobic surface domains whose relative sizes can be precisely tuned to give dimers, clusters, and larger micelle-like organizations. Using cryo-TEM imaging and ¹H DOSY NMR spectroscopy, we then provide an unprecedented “solution-state” picture of how the micelle-like structures respond to hydrophobic guests by encapsulating them within 250 nm diameter vesicles whose walls are comprised of amphiphilic AuNP membranes. These findings provide a versatile new option for transforming very small AuNPs into precisely tailored building blocks for the rational design of functional water-soluble assemblies.     

Structure of Reconstructed Cu(100) Surface Induced by Dissociative Adsorption of Gaseous Oxygen

The reconstructed structures of Cu(100) surface induced by O₂ dissociative adsorption wereinvestigated by low energy electron diffraction and scanning tunneling microscopy. At lower oxygen coverage, it was found that two reconstructed structures, i.e. c(2×2)-O and (√2×2√2)R45°-O are coexistent. The domain size of the c(2×2)-O structure decreased with the increasing of O₂ exposure. The reconstructed structure at very small coverage was also investigated and a “zigzag” structure was observed at this stage. The “zigzag” structure was identified as boundaries of local c(2×2) domains. It was found that the strip region shows much stronger molecule-substrate interaction than that of oxygen covered regions, making it a proper template for patterned organic films. The sequence of the thermal stability was found as zigzag structure>c(2×2)>(√2×2√2)R45°-O.     

Polyoxometalate‐Engineered Building Blocks with Gold Cores for the Self‐Assembly of Responsive Water‐Soluble Nanostructures

The controlled assembly of gold nanoparticles (AuNPs) with the size of quantum dots into predictable structures is extremely challenging as it requires the quantitatively and topologically precise placement of anisotropic domains on their small, approximately spherical surfaces. We herein address this problem by using polyoxometalate leaving groups to transform 2 nm diameter gold cores into reactive building blocks with hydrophilic and hydrophobic surface domains whose relative sizes can be precisely tuned to give dimers, clusters, and larger micelle‐like organizations. Using cryo‐TEM imaging and ¹H DOSY NMR spectroscopy, we then provide an unprecedented “solution‐state” picture of how the micelle‐like structures respond to hydrophobic guests by encapsulating them within 250 nm diameter vesicles whose walls are comprised of amphiphilic AuNP membranes. These findings provide a versatile new option for transforming very small AuNPs into precisely tailored building blocks for the rational design of functional water‐soluble assemblies.     

AFM nanoindentation of viscoelastic materials with large end‐radius probes

We used atomic force microscopy (AFM) nanoindentation to measure mechanical properties of polymers. Although AFM is generally acknowledged as a high‐resolution imaging tool, accurate quantification of AFM nanoindentation results is challenging. Two main challenges are determination of the projected area for objects as small as AFM tips and use of appropriate analysis methods for viscoelastic materials. We report significant accuracy improvements for modulus measurements when large end‐radius tips with appropriate cantilever stiffnesses are used for indentation. Using this approach, the instantaneous elastic modulus of four polymers we studied was measured within 30 to 40% of Dynamic Mechanical Analysis (DMA) results. The probes can, despite their size and very high stiffnesses, be used for imaging of very small domains in heterogeneous materials. For viscoelastic materials, we developed an AFM creep test to determine the instantaneous elastic modulus. The AFM method allows application of a nearly perfect stepload that facilitates data analysis based on hereditary integrals. Results for three polymers suggest that the observed creep in the materials has a strong plastic flow component even at small loads. In this respect, the spherical indenter tips behave like “sharp” indenters used in indentation studies with instrumented indenters. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1573–1587, 2009     

A Topological Approach to the Problem of Ring Structures

In the mechanized documentation of chemical literature, the definition of structural concept is very important. The usual for definitions for ring structures are inadequate. Essential ring structures are sometimes not recognized on the basis of these definitions and are therefore missed in a literature search. This is particularly true of bridged ring systems. The ring concept and ring condensation types are now redefined on a topological basis in the closest possible analogy to the intuitive approach of the chemist. In complicated molecular structures, these “fundamental rings” can be easily determined, either manually or by means of a programmed computer. The concept of the “ring complex” is defined and suggested as a preliminary screen in literature searches for ring structures. This will save machine time, and so reduce the cost of searches.     

Noncovalent self-assembly in aqueous medium: Mechanistic insights from time-resolved cryogenic electron microscopy

Supramolecular systems based on noncovalent bonds are adaptive due to the reversible nature of the noncovalent interactions, enabling stimuli responsiveness, self-healing, facile fabrication, and recyclability. There is much effort devoted to developing new synthetic tools in supramolecular chemistry. Progress in mechanistic understanding is of crucial importance for rational design targeting functional noncovalent nanoscale assemblies. So far, insufficient insight into evolution of noncovalent assemblies hindered our ability to make progress in the field.The typical paradigm in the case of non-covalent self-assembling systems involves the concept of rapid equilibration at ambient conditions. However, when strong noncovalent interactions are involved, kinetic control may dominate the outcome of the self-assembly processes. The ability of water to impose very strong hydrophobic interactions leads to slow transformations between different structural motifs, amenable to structural mechanistic studies. Cryo-TEM emerges as a method that enables direct structural analysis via imaging of “frozen” evolving assemblies. In this review we focus on cryo-TEM imaging of intermediate structures that evolve along a supramolecular transformation pathway. The structures investigated were trapped and directly visualized, in some cases with subnanometer resolution. Direct structural information obtained by time-resolved cryo-TEM proves to be critical for mechanistic understanding of complex multistep self-assembly processes. Such knowledge is necessary to address the challenge related to rational design of novel functional self-assembled materials.     

The nature of sites of absorption of low-molecular-mass compounds by butadiene–acrylonitrile copolymers

The rotational mobilities of the paramagnetic probes TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) and BZONO (4-benzoate-2,2,6,6-tetramethylpiperidine-1-oxyl) are studied via EPR spectroscopy and the equilibrium swelling of random and multiblock butadiene–acrylonitrile copolymers of various compositions and stereostructures of butadiene units in n-heptane, methyl acetate, and toluene are studied. The nature of defective regions sorbing low-molecular-mass compounds is ascertained. The rotational mobilities of the probes in defects of various structures are estimated. The sites of sorption are found to be identical in crosslinked and noncrosslinked elastomers. It is shown that the sorption of n-heptane and methyl acetate appears in the same defective regions as those of the TEMPO radical, while the sorption of toluene emerges in sorption sites where the value of free volume is sufficient for the sorption of the bulky radical BZONO. A decay in local molecular mobility in structural defects (“holes”) does not hinder the absorption of lowmolecular- mass compounds if the free volume is sufficient.     

Atomic resolution electron microscopy of small metal clusters

Atomic resolution imaging of cluster structures has been performed with high resolution transmission electron microscopy (HRTEM). Metal particles of the sizes 1 nanometer to tens of nanometers have been surface profile imaged on different supports; like zeolites, cordierite and amorphous carbon. It is shown that organic ligands in Schmid-clusters coordinated to the metal surface are desorbed or destroyed by the electron beam. Dynamic events on the surfaces and in the bulk of small metal particles have been recorded for small crystals of Au, Pt, Rh and Pb and can be classified under three headings; The smaller the crystals are the faster rearrangements of the crystal structure; “clouds” of atoms existing outside some surfaces are involved in extensive structural rearrangements of the surface or crystal surface growth; localized atom hopping on surfaces during crystal growth and desorption also occurs.     

Progress in the direct structural characterization of fibrous amphiphilic supramolecular assemblies in solution by transmission electron microscopic techniques

The self-assembly of amphiphilic molecules into fibrous structures has been the subject of numerous studies over past decades due to various current and promising technical applications. Although very different in their head group chemistry many natural as well as synthetic amphiphilic compounds derived from carbohydrates, carbocyanine dyes, or amino acids tend to form fibrous structures by molecular self-assembly in water predominantly twisted ribbons or tubes. Often a transition between these assembly structures is observed, which is a phenomenon already theoretically approached by Wolfgang Helfrich and still focus point in current research. With the development of suitable sample preparation and electron optical imaging techniques, cryogenic transmission electron microscopy (cryo-TEM) in combination with three-dimensional (3D) reconstruction techniques has become a particular popular direct characterization technique for supramolecular assemblies in general. Here we review the recent progress in deriving precise structural information from cryo-TEM data of particularly fibrous structures preferably in three dimensions.     

Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.     

Structures lamellaires: Syntaxie,polytypie et non-stoechiométrie

The paper recalls elementary principles useful for the understanding of some types of nonstoichiometry in the solid state. The structures of layered compounds are mostly characterized by the existence of layered “molecular” entities exhibiting a simple type of bonding; in between are inserted, depending on the case, cations, anions, structural frameworks, or molecules. The layers have a quaternary or a ternary symmetry; in the last case the structures can be polytypic. The phenomenon of syntaxy occurs between polymorphs or between species with different chemical compositions but with structural affinities (identical atomic planes). In some cases an ordered syntaxy between structural blocks yields the chemical compositions of the multiple phases observed for some nonstoichiometric systems, for instance rare earth ones. Ordered syntaxy and polytypism, which can occur simultaneously, give a regular repetition of structural or chemical elements over very long crystalline distances. Those phenomena of order in solids, as yet unexplained, recall ordering phenomena observed in the scope of biological chemistry.     

Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge

Induced fit or protein flexibility can make a given structure less useful for docking and/or scoring. The 2015 Drug Design Data Resource (D3R) Grand Challenge provided a unique opportunity to prospectively test optimal strategies for virtual screening in these type of targets: heat shock protein 90 (HSP90), a protein with multiple ligand-induced binding modes; and mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), a kinase with a large flexible pocket. Using previously known co-crystal structures, we tested predictions from methods that keep the receptor structure fixed and used (a) multiple receptor/ligand co-crystals as binding templates for minimization or docking (“close”), (b) methods that align or dock to a single receptor (“cross”), and (c) a hybrid approach that chose from multiple bound ligands as initial templates for minimization to a single receptor (“min-cross”). Pose prediction using our “close” models resulted in average ligand RMSDs of 0.32 and 1.6 Å for HSP90 and MAP4K4, respectively, the most accurate models of the community-wide challenge. On the other hand, affinity ranking using our “cross” methods performed well overall despite the fact that a fixed receptor cannot model ligand-induced structural changes,. In addition, “close” methods that leverage the co-crystals of the different binding modes of HSP90 also predicted the best affinity ranking. Our studies suggest that analysis of changes on the receptor structure upon ligand binding can help select an optimal virtual screening strategy.     

Structure Formation and Molecular Mobility in Water and in Aqueous Solutions

The study of the structure of water and of aqueous solutions has recently received new impetus from the efforts at commercial desalineation of sea water and from developments in molecular biology. The current view that, apart from single molecules, water contains only one type of structural element, namely “flickering” network structures with tetrahedrally hydrogen-bonded water molecules (two-states model) is proving inadequate in the interpretation of new experimental data and in the calculation of thermodynamic functions. After a critical discussion of the basis of this model and of the concept of hydrogen bonds, a second kind of structural element, i.e. a third state, is suggested: small aggregates of molecules containing mainly non-tetrahedral hydrogen bonds as well as some tetrahedral ones, and packed more densely than allowed by the lattice-like structure. These aggregates – dimers to hexamers – can be regarded as the primary products of disruption of the network structures, and displace the latter as structural components in water with increasing temperature or concentration of solutes. This “combined” model allows a consistent interpretation of the properties of water and of the various effects of dissolved substances.     

“Printing” DNA Strand Patterns on Small Molecules with Control of Valency,Directionality, and Sequence

The incorporation of synthetic molecules as corner units in DNA structures has been of interest over the last two decades. In this work, we present a facile method for generating branched small molecule‐DNA hybrids with controllable valency, different sequences, and directionalities (5′–3′) using a “printing” process from a simple 3‐way junction structure. We also show that the DNA‐imprinted small molecule can be extended asymmetrically using polymerase chain reaction (PCR) and can be replicated chemically. This strategy provides opportunities to achieve new structural motifs in DNA nanotechnology and introduce new functionalities to DNA nanostructures.     

“Printing” DNA Strand Patterns on Small Molecules with Control of Valency,Directionality, and Sequence

The incorporation of synthetic molecules as corner units in DNA structures has been of interest over the last two decades. In this work, we present a facile method for generating branched small molecule‐DNA hybrids with controllable valency, different sequences, and directionalities (5′–3′) using a “printing” process from a simple 3‐way junction structure. We also show that the DNA‐imprinted small molecule can be extended asymmetrically using polymerase chain reaction (PCR) and can be replicated chemically. This strategy provides opportunities to achieve new structural motifs in DNA nanotechnology and introduce new functionalities to DNA nanostructures.     

Genealogically directed syntheses (polymerizations): Direct evidence by electrospray mass spectroscopy

From a synthetic perspective, divergent dendrimer syntheses are often presented as idealized hyperbranched growth processes leading to perfect dendritic structures. Experimentally it has been found that in addition to ideal structures, varying amounts of structural errors are produced at each growth stage (generation). These defects (mutants) are created as a function of processing conditions and generation specific steric effects. This investigation focused on the divergent synthesis of Starburstr̀ polyamidoamine dendrimers** and the use of electrospray mass spectroscopy for appraising ideal structure/defect ratios as a function of generation. With this methodology, initial defect types and so called “defect propagation chains” have been identified and characterized. These hyperbranched mutation (defect) patterns provide ample evidence for the “genealogically directed” character of this divergent polymerization strategy.     

The electron microscope characterization of the fine structure of nylon 6: I. The supermolecular structure in melt-cast,isotropic bulk material

The application of phosphotungstic acid (PTA) as a staining agent with appropriate hardening procedures and accurate ultra-thin sectioning has enabled the direct transmission electron microscope (TEM) investigation to be carried out on the lamellar fine structure of bulk nylon 6. Details of the organization of the crystal lamellae within spherulites and other morphological structures, their shape and, especially, their dimensions were revealed and the mean structural long period was determined. Interspherulitic regions without any indication of crystalline ordering could be observed in samples which were rapidly cooled from the melt. The investigations on bulk material were completed by observations on solution-grown thin films. Optical diffraction (OD) was used for evaluating the electron micrographs; the results were compared with the data from small angle X-ray scattering (SAXS).