Halogen bonds in 2D supramolecular self-assembly of organic semiconductors

Weak interactions between bromine, sulphur, and hydrogen are shown to stabilize 2D supramolecular monolayers at the liquid–solid interface. Three different thiophene-based semiconducting organic molecules assemble into close-packed ultrathin ordered layers. A combination of scanning tunneling microscopy (STM) and density functional theory (DFT) elucidates the interactions within the monolayer. Electrostatic interactions are identified as the driving force for intermolecular Br⋯Br and Br⋯H bonding. We find that the S⋯S interactions of the 2D supramolecular layers correlate with the hole mobilities of thin film transistors of the same materials.

Two-dimensional self-assembly of a symmetry-reduced tricarboxylic acid

Investigations of the self-assembly of simple molecules at the solution/solid interface can provide useful insight into the general principles governing supramolecular chemistry in two dimensions. Here, we report on the assembly of 3,4′,5-biphenyl tricarboxylic acid (H3BHTC), a small hydrogen bonding unit related to the much-studied 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), which we investigate using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. STM images show that H3BHTC assembles by itself into an offset zigzag chain structure that maximizes the surface molecular density in favor of maximizing the number density of strong cyclic hydrogen bonds between the carboxylic groups. The offset geometry creates “sticky” pores that promote solvent coadsorption. Adding coronene to the molecular solution produces a transformation to a high-symmetry host–guest lattice stabilized by a dimeric/trimeric hydrogen bonding motif similar to the TMA flower structure. Finally, we show that the H3BHTC lattice firmly immobilizes the guest coronene molecules, allowing for high-resolution imaging of the coronene structure.

Unprecedented transformation of tetrathienoanthracene into pentacene on Ni(111)

The imaging and characterization of single-molecule reaction events is essential to both extending our basic understanding of chemistry and applying this understanding to challenges at the frontiers of technology, for example, in nanoelectronics. Specifically, understanding the behavior of individual molecules can elucidate processes critical to the controlled synthesis of materials for applications in multiple nanoscale technologies. Here, we report the synthesis of an important semiconducting organic molecule through an unprecedented reaction observed with submolecular resolution by scanning tunneling microscopy (STM) under ultrahigh vacuum (UHV) conditions. Our images reveal a sulfur abstraction and cyclization reaction that converts tetrathienoanthracene precursors into pentacene on the Ni(111) surface. The identity of the final reaction product was confirmed by time-of-flight secondary ion mass spectrometry (TOF-SIMS). This reaction has no known literature analogue, and highlights the power of local-probe techniques for exploring new chemical pathways.

Covalently bonded networks through surface-confined polymerization

The prospect of synthesizing ordered, covalently bonded structures directly on a surface has recently attracted considerable attention due to its fundamental interest and for potential applications in electronics and photonics. This prospective article focuses on efforts to synthesize and characterize epitaxial one- and two-dimensional (1D and 2D, respectively) polymeric networks on single crystal surfaces. Recent studies, mostly performed using scanning tunneling microscopy (STM), demonstrate the ability to induce polymerization based on Ullmann coupling, thermal dehalogenation and dehydration reactions. The 2D polymer networks synthesized to date have exhibited structural limitations and have been shown to form only small domains on the surface. We discuss different approaches to control 1D and 2D polymerization, with particular emphasis on the surface phenomena that are critical to the formation of larger ordered domains.

Self-assembly of a halogenated molecule on oxide-passivated Cu(110)

The supramolecular self-assembly of brominated molecules was investigated and compared on Cu(110) and Cu(110)[BOND]O(2×1) surfaces under ultrahigh vacuum. By using scanning tunnelling microscopy, we show that brominated molecules form a disordered structure on Cu(110), whereas a well-ordered supramolecular network is observed on the Cu(110)[BOND]O(2×1) surface. The different adsorption behaviors of these two surfaces are described in terms of weakened molecule–substrate interactions on Cu(110)[BOND]O(2×1) as opposed to bare Cu(110). The effect of oxygen-passivation is to suppress debromination and it can be a convenient approach for investigating other self-assembly processes on copper-based substrates.

Indium clusters on the Ge (5× 5) wetting layer of Si (111)- 7× 7

The adsorption of In on the Si(111)−Ge(5×5) surface reconstruction has been studied with scanning tunneling microscopy and ab initio calculations to investigate the possibility of using this reconstruction as a template for cluster formation. As with In adsorption on Si(111)−7×7 at low substrate temperatures and low In fluences, the In adatoms are found to preferentially adsorb on the faulted half-unit cell. However, in contrast to In adsorption on Si(111)−7×7, the In adatoms are also frequently found in the unfaulted half-unit cell at low coverages. The filling of unfaulted unit cell halves is primarily due to the formation of large clusters that span multiple substrate half-unit cells. Moreover, many of the faulted half-unit cells have a streaked appearance that indicates that surface atoms within them are mobile.

Tip-induced C--H activation and oligomerization of thienoanthracenes

The tip of a scanning tunneling microscope (STM) can be used to dehydrogenate freely-diffusing tetrathienoanthracene (TTA) molecules on Cu(111), trapping the molecules into metal-coordinated oligomeric structures. The process proceeds at bias voltages above ∼3 V and produces organometallic structures identical to those resulting from the thermally-activated cross-coupling of a halogenated analogue. The process appears to be substrate dependent: no oligomerization was observed on Ag(111) or HOPG. This approach demonstrates the possibility of controlled synthesis and nanoscale patterning of 2D oligomer structures on selected surfaces.

Substrate, molecular structure, and solvent effects in 2D self-assembly via hydrogen and halogen bonding

Recently, halogen···halogen interactions have been demonstrated to stabilize two-dimensional supramolecular assemblies at the liquid–solid interface. Here we study the effect of changing the halogen, and report on the 2D supramolecular structures obtained by the adsorption of 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) and 2,4,6-tris(4-iodophenyl)-1,3,5-triazine (TIPT) on both highly oriented pyrolytic graphite and the (111) facet of a gold single crystal. These molecular systems were investigated by combining room-temperature scanning tunneling microscopy in ambient conditions with density functional theory, and are compared to results reported in the literature for the similar molecules 1,3,5-tri(4-bromophenyl)benzene (TBPB) and 1,3,5-tri(4-iodophenyl)benzene (TIPB). We find that the substrate exerts a much stronger effect than the nature of the halogen atoms in the molecular building blocks. Our results indicate that the triazine core, which renders TBPT and TIPT stiff and planar, leads to stronger adsorption energies and hence structures that are different from those found for TBPB and TIPB. On the reconstructed Au(111) surface we find that the TBPT network is sensitive to the fcc- and hcp-stacked regions, indicating a significant substrate effect. This makes TBPT the first molecule reported to form a continuous monolayer at room temperature in which molecular packing is altered on the differently reconstructed regions of the Au(111) surface. Solvent-dependent polymorphs with solvent coadsorption were observed for TBPT on HOPG. This is the first example of a multicomponent self-assembled molecular networks involving the rare cyclic, hydrogen-bonded hexamer of carboxylic groups, R66(24) synthon.

Genetic association analysis of miRNA SNPs implicates MIR145 in breast cancer susceptibility

Background MicroRNAs (miRNAs) are important small non-coding RNA molecules that regulate gene expression in cellular processes related to the pathogenesis of cancer. Genetic variation in miRNA genes could impact their synthesis and cellular effects and single nucleotide polymorphisms (SNPs) are one example of genetic variants studied in relation to breast cancer. Studies aimed at identifying miRNA SNPs (miR-SNPs) associated with breast malignancies could lead towards further understanding of the disease and to develop clinical applications for early diagnosis and treatment. Methods We genotyped a panel of 24 miR-SNPs using multiplex PCR and chip-based matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis in two Caucasian breast cancer case control populations (Primary population: 173 cases and 187 controls and secondary population: 679 cases and 301 controls). Association to breast cancer susceptibility was determined using chi-square (X 2 ) and odds ratio (OR) analysis. Results Statistical analysis showed six miR-SNPs to be non-polymorphic and twelve of our selected miR-SNPs to have no association with breast cancer risk. However, we were able to show association between rs353291 (located in MIR145) and the risk of developing breast cancer in two independent case control cohorts (p = 0.041 and p = 0.023). Conclusions Our study is the first to report an association between a miR-SNP in MIR145 and breast cancer risk in individuals of Caucasian background. This finding requires further validation through genotyping of larger cohorts or in individuals of different ethnicities to determine the potential significance of this finding as well as studies aimed to determine functional significance. Keywords: Association analysis; Breast cancer; microRNA; miR-SNPs; MIR145

KRAS variation and risk of endometriosis

Endometriosis is a common gynaecological disease with symptoms of pelvic pain and infertility which affects 7-10% of women in their reproductive years. Activation of an oncogenic allele of Kirsten rat sarcoma viral oncogene homologue (KRAS) in the reproductive tract of mice resulted in the development of endometriosis. We hypothesized that variation in KRAS may influence risk of endometriosis in humans. Thirty tagSNPs spanning a region of 60.7 kb across the KRAS locus were genotyped using iPLEX chemistry on a MALDI-TOF MassARRAY platform in 959 endometriosis cases and 959 unrelated controls, and data were analysed for association with endometriosis. Genotypes were obtained for most individuals with a mean completion rate of 99.1%. We identified six haplotype blocks across the KRAS locus in our sample. There were no significant differences between cases and controls in the frequencies of individual single-nucleotide polymorphisms (SNPs) or haplotypes. We also developed a rapid method to screen for 11 common KRAS and BRAF mutations on the Sequenom MassARRAY system. The assay detected all mutations previously identified by direct sequencing in a panel of positive controls. No germline variants for KRAS or BRAF were detected. Our results demonstrate that any risk of endometriosis in women because of common variation in KRAS must be very small.

Thin nanoporous metal-insulator-metal membranes

Insulating nanoporous materials are promising platforms for soft-ionizing membranes; however, improvement in fabrication processes and the quality and high breakdown resistance of the thin insulator layers are needed for high integration and performance. Here, scalable fabrication of highly porous, thin, silicon dioxide membranes with controlled thickness is demonstrated using plasma-enhanced chemical-vapor-deposition. The fabricated membranes exhibit good insulating properties with a breakdown voltage of 1 × 107 V/cm. Our calculations suggest that the average electric field inside a nanopore of the membranes can be as high as 1 × 106 V/cm; sufficient for ionization of wide range of molecules. These metal–insulator–metal nanoporous arrays are promising for applications such soft ionizing membranes for mass spectroscopy.