2H‐Tetrakis(3,5‐di‐tert‐butyl)phenylporphyrin on a Cu(110) Surface: Room‐Temperature Self‐Metalation and Surface‐Reconstruction‐Facilitated Self‐Assembly

The adsorption behavior of 2H‐tetrakis(3,5‐di‐tert‐butyl)phenylporphyrin (2HTTBPP) on Cu(110) and Cu(110)–(2×1)O surfaces have been investigated by using variable‐temperature scanning tunneling microscopy (STM) under ultrahigh vacuum conditions. On the bare Cu(110) surface, individual 2HTTBPP molecules are observed. These molecules are immobilized on the surface with a particular orientation with respect to the crystallographic directions of the Cu(110) surface and do not form supramolecular aggregates up to full monolayer coverage. In contrast, a chiral supramolecular structure is formed on the Cu(110)–(2×1)O surface, which is stabilized by van der Waals interactions between the tert‐butyl groups of neighboring molecules. These findings are explained by weakened molecule–substrate interactions on the Cu(110)–(2×1)O surface relative to the bare Cu(110) surface. By comparison with the corresponding results of Cu–tetrakis(3,5‐di‐tert‐butyl)phenylporphyrin (CuTTBPP) on Cu(110) and Cu(110)–(2×1)O surfaces, we find that the 2HTTBPP molecules can self‐metalate on both surfaces with copper atoms from the substrate at room temperature (RT). The possible origins of the self‐metalation reaction at RT are discussed. Finally, peculiar irreversible temperature‐dependent switching of the intramolecular conformations of the investigated molecules on the Cu(110) surface was observed and interpreted.     

Site‐Specific Labeling of Affimers for DNA‐PAINT Microscopy

Optical super‐resolution techniques allow fluorescence imaging below the classical diffraction limit of light. From a technology standpoint, recent methods are approaching molecular‐scale spatial resolution. However, this remarkable achievement is not easily translated to imaging of cellular components, since current labeling approaches are limited by either large label sizes (antibodies) or the sparse availability of small and efficient binders (nanobodies, aptamers, genetically‐encoded tags). In this work, we combined recently developed Affimer reagents with site‐specific DNA modification for high‐efficiency labeling and imaging using DNA‐PAINT. We assayed our approach using an actin Affimer. The small DNA‐conjugated affinity binders could provide a solution for efficient multitarget super‐resolution imaging in the future.     

Torands Revisited: Metal Sequestration and Self‐Assembly of Cyclo‐2,9‐tris‐1,10‐phenanthroline Hexaaza Macrocycles

A series of novel toroidal cyclo‐2,9‐tris‐1,10‐phenanthroline macrocycles with an unusual hexaaza cavity are reported. Nickel‐mediated Yamamoto aryl–aryl coupling was found to be a versatile tool for the cyclotrimerization of functionalized 1,10‐phenathroline precursors. Due to the now improved processability, both liquid‐crystalline behavior in the bulk phase and two‐dimensional self‐assembly at the molecular level could be studied, for the first time, for a torand system. The macrocycles exhibited a strong affinity for the complexation of different metal cations, as evidenced by MALDI‐TOF analysis and spectroscopic methods. Experimental results were correlated to an extensive computational study of the cyclo‐2,9‐tris‐1,10‐phenanthroline cavity and its binding mode for metal cations. Due to the combination of several interesting features, toroidal macrocycles may find future applications in the field of ion and charge transport through molecular channels, as well as for chemical sensing and molecular writing in surface‐confined monolayers under STM conditions.     

Structural polymorphism in poly(dodecamethylen‐di‐O‐methyl‐L‐tartaramide)

Structural characterization of poly(dodecamethylen‐di‐O‐methyl‐L‐tartaramide) was carried out with optical microscopy, thermal analysis, X‐ray diffraction, and electron microscopy. Two different crystalline forms were found in accordance with the thermograms, powder and fiber X‐ray diffraction diagrams. The electron microscopy allows corroboration of the morphological and crystallographic differences. Molecular modeling was used to conclude the structural analogies and differences between the two crystalline forms that were related to the chain packing and orientation in the crystal cell, respectively. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2523–2530, 2002     

Highly Intact and Pure Oxo‐Functionalized Graphene: Synthesis and Electron‐Beam‐Induced Reduction

Controlling the chemistry of graphene is necessary to enable applications in materials and life sciences. Research beyond graphene oxide is targeted to avoid the highly defective character of the carbon framework. Herein, we show how to optimize the synthesis of oxo‐functionalized graphene (oxo‐G) to prepare high‐quality monolayer flakes that even allow for direct transmission electron microscopy investigation at atomic resolution (HRTEM). The role of undesired residuals is addressed and sources are eliminated. HRTEM provides clear evidence for the exceptional integrity of the carbon framework of such oxo‐G sheets. The patchy distribution of oxo‐functionality on the nm‐scale, observed on our highly clean oxo‐G sheets, corroborates theoretical predictions. Moreover, defined electron‐beam irradiation facilitates gentle de‐functionalization of oxo‐G sheets, a new route towards clean graphene, which is a breakthrough for localized graphene chemistry.     

A General Mechanism of Photoconversion of Green‐to‐Red Fluorescent Proteins Based on Blue and Infrared Light Reduces Phototoxicity in Live‐Cell Single‐Molecule Imaging

Photoconversion of fluorescent proteins by blue and complementary near‐infrared light, termed primed conversion (PC), is a mechanism recently discovered for Dendra2. We demonstrate that controlling the conformation of arginine at residue 66 by threonine at residue 69 of fluorescent proteins from Anthozoan families (Dendra2, mMaple, Eos, mKikGR, pcDronpa protein families) represents a general route to facilitate PC. Mutations of alanine 159 or serine 173, which are known to influence chromophore flexibility and allow for reversible photoswitching, prevent PC. In addition, we report enhanced photoconversion for pcDronpa variants with asparagine 116. We demonstrate live‐cell single‐molecule imaging with reduced phototoxicity using PC and record trajectories of RNA polymerase in Escherichia coli cells.     

Two‐Dimensional Oligo(phenylene‐ethynylene‐butadiynylene)s: All‐Covalent Nanoscale Spoked Wheels

Round and round : Covalently bound spokes induce an efficient template‐directed cyclization towards a rigid molecular wheel (see figure) and afford dramatically increased shape‐persistence properties compared with non‐strutted macrocycles.

     

“Reduced” Coumarin Dyes with an O‐Phosphorylated 2,2‐Dimethyl‐4‐(hydroxymethyl)‐1,2,3,4‐tetrahydroquinoline Fragment: Synthesis,Spectra, and STED Microscopy

Large Stokes‐shift coumarin dyes with an O‐phosphorylated 4‐(hydroxymethyl)‐2,2‐dimethyl‐1,2,3,4‐tetrahydroquinoline fragment emitting in the blue, green, and red regions of the visible spectrum were synthesized. For this purpose, N‐substituted and O‐protected 1,2‐dihydro‐7‐hydroxy‐2,2,4‐trimethylquinoline was oxidized with SeO₂ to the corresponding α,β‐unsaturated aldehyde and then reduced with NaBH₄ in a “one‐pot” fashion to yield N‐substituted and 7‐O‐protected 4‐(hydroxymethyl)‐7‐hydroxy‐2,2‐dimethyl‐1,2,3,4‐tetrahydroquinoline as a common precursor to all the coumarin dyes reported here. The photophysical properties of the new dyes (“reduced coumarins”) and 1,2‐dihydroquinoline analogues (formal precursors) with a trisubstituted C=C bond were compared. The “reduced coumarins” were found to be more photoresistant and brighter than their 1,2‐dihydroquinoline counterparts. Free carboxylate analogues, as well as their antibody conjugates (obtained from N‐hydroxysuccinimidyl esters) were also prepared. All studied conjugates with secondary antibodies afforded high specificity and were suitable for fluorescence microscopy. The red‐emitting coumarin dye bearing a betaine fragment at the C‐3‐position showed excellent performance in stimulation emission depletion (STED) microscopy.     

Morphological mapping and analysis of poly[styrene‐b‐(ethylene‐co‐butylene)‐b‐styrene] and its clay nanocomposites by atomic force microscopy

Atomic force microscopy was successfully applied for comprehensive nanoscale surface and bulk morphological characterization of thermoplastic elastomeric triblock copolymers: poly[styrene‐b‐(ethylene‐co‐butylene)‐b‐styrene] (SEBS) having different block lengths and their clay based nanocomposites. Commercially available Cloisite®20A and octadecyl (C₁₈) ammonium ion modified montmorillonite clay (OC) prepared in our laboratory by cation exchange reaction were used. The phase detected images in the tapping mode atomic force microscopy exhibited a well‐ordered phase separated morphology consisting of bright nanophasic domains corresponding to hard component and darker domains corresponding to softer rubbery ethylene‐co‐butylene (PEB) lamella for all the neat triblock copolymers. This lamellar morphology gave a domain width of 19–23 nm for styrenic nanophase and 12–15 nm for ethylene‐co‐butylene phase of SEBS having end to mid block length ratio of 30:70 and block molecular weights of 8800–41,200–8800. On increasing the ratio of block lengths of the polymer matrix and the selectivity of the solvent toward the blocks used for casting, the morphological features of the resultant films altered along with change in domain thickness. The phase images showed position and distribution of the brightest clay stacks in the dark‐bright contrast of the base matrix of the nanocomposite. Exfoliated and intercalated‐exfoliated morphology obtained in the case of Cloisite®20A and OC‐based SEBS nanocomposites, respectively, is further supported by X‐ ray diffraction and transmission electron microscopy studies. The lamellar thickness of the soft phases widened to 50–75 nm, where the layered clay silicates (40–54 nm in length and 4–17 nm in width) were embedded in the soft rubbery phases in the block copolymeric matrix of the nanocomposite. The marginally thicker width of the hard styrenic phases and slightly shrinked width of the soft rubbery lamella can be observed from the regions where no nanofiller is present. Distinct differences in bulk morphologies of the nanocomposites prepared in the melt and the solution processes were obtained with nanocomposites. The presence of clay particles was evident from the almost zero pull‐off and snap‐in force in the force‐distance analysis of SEBS based nanocomposite. This analysis also revealed stronger tip interaction resulting in highest contact and adhesive forces with the softer PEB region relative to the harder PS region. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 52–66, 2007     

Self‐Assembly of Fivefold‐Symmetric Molecules on a Threefold‐Symmetric Surface

Buckybowls : The adsorption of penta‐tert‐butylcorannulene, a molecule with fivefold symmetry, on Cu(111), a surface with threefold symmetry, is investigated by scanning tunneling microscopy complemented by structure calculations. The symmetry mismatch is resolved by the formation of threefold‐symmetric subunits consisting of three molecules, which combine with single molecules to form a nearly perfect filling of the plane (see picture).

     

Direct Formation of C−C Triple‐Bonded Structural Motifs by On‐Surface Dehalogenative Homocouplings of Tribromomethyl‐Substituted Arenes

On‐surface synthesis shows significant potential in constructing novel nanostructures/nanomaterials, which has been intensely studied in recent years. The formation of acetylenic scaffolds provides an important route to the fabrication of emerging carbon nanostructures, including carbyne, graphyne, and graphdiyne, which feature chemically vulnerable sp‐hybridized carbon atoms. Herein, we designed and synthesized a tribromomethyl‐substituted compound. By using a combination of high‐resolution scanning tunneling microscopy, non‐contact atomic force microscopy, and density functional theory calculations, we demonstrated that it is feasible to convert these compounds directly into C?C triple‐bonded structural motifs by on‐surface dehalogenative homocoupling reactions. Concurrently, sp³‐hybridized carbon atoms are converted into sp‐hybridized ones, that is, an alkyl group is transformed into an alkynyl moiety. Moreover, we achieved the formation of dimer structures, one‐dimensional molecular wires, and two‐dimensional molecular networks on Au(111) surfaces, which should inspire further studies towards two‐dimensional graphyne structures.     

Surface‐Modifiable Free‐Floating Films Formed by Multiway Connection of Collagen‐Like Triple‐Helical Peptides

Square‐millimeter‐sized free‐floating translucent films are formed in physiological buffer by multiway connections between biotinylated collagen‐like triple‐helical peptides and avidin. Although the compositions of the films are almost constant, regardless of the ratios of the components loaded, their thicknesses can be controlled by the concentrations of the components. The film surfaces can be further modified by taking advantage of exposed biotin (or avidin) functionalities. The self‐assembled films could serve as novel materials in biomedical and biosensing applications.     

High‐Silica Zeolite SSZ‐61 with Dumbbell‐Shaped Extra‐Large‐Pore Channels

The synthesis of the high‐silica zeolite SSZ‐61 using a particularly bulky polycyclic structure‐directing agent and the subsequent elucidation of its unusual framework structure with extra‐large dumbbell‐shaped pore openings are described. By using information derived from a variety of X‐ray powder diffraction and electron microscopy techniques, the complex framework structure, with 20 Si atoms in the asymmetric unit, could be determined and the full structure refined. The Si atoms at the waist of the dumbbell are only three‐connected and are bonded to terminal O atoms pointing into the channel. Unlike the six previously reported extra‐large‐pore zeolites, SSZ‐61 contains no heteroatoms in the framework and can be calcined easily. This, coupled with the possibility of inserting a catalytically active center in the channel between the terminal O atoms in place of H⁺, afford SSZ‐61 intriguing potential for catalytic applications.     

On‐Surface Self‐Assembly of a C3‐Symmetric π‐Conjugated Molecule Family Studied by STM: Two‐Dimensional Nanoporous Frameworks

The on‐surface self‐assembled behavior of four C ₃‐symmetric π‐conjugated planar molecules ( Tp , T12 , T18 , and Ex ) has been investigated. These molecules are excellent building blocks for the construction of noncovalent organic frameworks in the bulk phase. Their hydrogen‐bonded 2D on‐surface self‐assemblies are observed under STM at the solid/liquid interface; these structures are very different to those in the bulk crystal. Upon combining the results of STM measurements and DFT calculations, the formation mechanism of different assemblies is revealed; in particular, the critical role of hydrogen bonding in the assemblies. This research provides us with not only a deep insight into the self‐assembled behavior of these novel functional molecules, but also a convenient approach toward the construction of 2D multiporous networks.     

Ionic aggregates in Zn‐ and Na‐neutralized poly(ethylene‐ran‐methacrylic acid) blown films

The morphology of ionic aggregates in semicrystalline Zn‐ and Na‐neutralized poly(ethylene‐ran‐methacrylic acid) (EMAA) ionomer blown films has been explored with scanning transmission electron microscopy (STEM) and small angle X‐ray scattering. The ionic aggregates of Zn‐EMAA are spherical, monodisperse, and uniformly distributed in as‐extruded pellets and blown films prepared at low and high blow‐up ratio. Thus, although the biaxial stresses of film blowing are sufficient to alter the PE superstructure, the ionic aggregates in Zn‐EMAA are unaffected. In contrast, the morphology of Na‐EMAA as detected by STEM changes from featureless in the as‐extruded pellets to a heterogeneous distribution of Na‐rich aggregates in the blown films. This transformation in Na‐EMAA morphology is consistent with our earlier study of quiescent annealing, suggesting that the morphological change is the result of thermal processing rather than the biaxial stresses of film blowing. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3549–3554, 2005     

Solvent‐ and interface‐induced surface segregation in blends of isotactic polypropylene with poly(ethylene‐co‐propylene) rubber

The surface compositions and morphologies of melt‐quenched blends of isotactic polypropylene (iPP) with aspecific poly(ethylene‐co‐propylene) rubber (aEPR) were characterized by atomic force microscopy, optical microscopy, and X‐ray photoelectron spectroscopy. The surface morphologies and compositions formed in the melt are frozen‐in by crystallization of the iPP component and, depending on the processing conditions, are enriched in iPP or aEPR or contain a phase‐separated mix of iPP and aEPR. Enrichment of iPP is observed for blends melted in open air, in agreement with earlier work showing the high surface activity of atactic polypropylene at open interfaces. Surface segregation of iPP is suppressed at confined interfaces. Blends melt‐pressed between hydrophilic and hydrophobic substrates have phase‐separated iPP and aEPR domains present at the surface, which grow in size as the melt time increases. Surface enrichment of aEPR is observed after exposing melt‐pressed blends to n‐hexane vapor, which preferentially solvates aEPR and draws it to the surface. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 421–432, 2004