Influence of Structural Variation on the Solid-State Properties of Diketopyrrolopyrrole-Based Oligophenylenethiophenes: Single-Crystal Structures, Thermal Properties, Optical Bandgaps, Energy Levels, Film Morphology, and Hole Mobility

Five new compounds, based on diketopyrrolopyrrole (DPP) and phenylene thiophene (PT) moieties, were synthesized to investigate the effect of structural variations on solid state properties, such as single-crystal structures, optical absorption, energy levels, thermal phase transitions, film morphology, and hole mobility. The molecular structures were modified by means of (i) backbone length by changing the number of thiophenes on both sides of DPP, (ii) alkyl substitution (<i>n</i>-hexyl or ethylhexyl) on DPP, and (iii) the presence of an <i>n</i>-hexyl group at the end of the molecular backbone. These DPP-based oligophenylenethiophenes were systematically characterized by UV–visible spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), cyclic voltammetry (CV), ultraviolet photoelectron spectroscopy (UPS), atomic force microscopy (AFM), and hole-only diodes. Single-crystal structures were provided to probe insight into structure–property relationships at a molecule level resolution. This work demonstrates the significance of alkyl substitution as well as backbone length in tuning material’s solid-state properties

Influence of Structural Variation on the Solid-State Properties of Diketopyrrolopyrrole-Based Oligophenylenethiophenes: Single-Crystal Structures, Thermal Properties, Optical Bandgaps, Energy Levels, Film Morphology, and Hole Mobility

Five new compounds, based on diketopyrrolopyrrole (DPP) and phenylene thiophene (PT) moieties, were synthesized to investigate the effect of structural variations on solid state properties, such as single-crystal structures, optical absorption, energy levels, thermal phase transitions, film morphology, and hole mobility. The molecular structures were modified by means of (i) backbone length by changing the number of thiophenes on both sides of DPP, (ii) alkyl substitution (<i>n</i>-hexyl or ethylhexyl) on DPP, and (iii) the presence of an <i>n</i>-hexyl group at the end of the molecular backbone. These DPP-based oligophenylenethiophenes were systematically characterized by UV–visible spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), cyclic voltammetry (CV), ultraviolet photoelectron spectroscopy (UPS), atomic force microscopy (AFM), and hole-only diodes. Single-crystal structures were provided to probe insight into structure–property relationships at a molecule level resolution. This work demonstrates the significance of alkyl substitution as well as backbone length in tuning material’s solid-state properties

Statistically overrepresented pathways for KR12-bound genes, compared to members in the Ras pathway (hsa04014) alone.

<p>Fold enrichment between two groups have a <i>χ</i>^<i>2</i> statistic of 30.958 (<i>p</i> ~ 1.43 × 10⁻⁴).</p

Next-generation sequencing with biotinylated KR12.

<p>(A) Synthetic scheme of KR12 from the non-biotinylated precursor KR12 N/B, with pyrroles and imidazoles colored in blue and red, respectively. (B) HPLC retention time diagram (upper right) and mass spectrum (LC-MS) of KR12. (C) WST assay of LS180 cells at 300 and 1000 nM dosage of KR12 (black) compared to the non-biotinylated precursor (KR12 N/B, gray) and DMSO only (white); error bars indicate ±1 SEM; n.s., no significance by two-sample Welch’s <i>t</i>-test.</p

KR12 binding in the human colorectal carcinoma LS180 genome.

<p>(A) Workflow to identify KR12 binding sites in the LS180 genome by IonTorrent sequencing. Cells are administered with KR12 (500 nM, 6 h) prior to genomic DNA extraction and fragmentation by sonication. Enrichment by streptavidin allows the capture of KR12-bound nucleotides. A computational routine maps candidate regions in sequencing data, followed by site calling via motif matching and statistical validation. Subsequent microarray analyses provide the means to confirm binding data with genome-level changes. (B) Sample sequencing coverage of <i>PIK3CA</i> and <i>KRAS</i>, genes with KR12 binding sites (“KR12+”), and for reference, a predicted site by motif matching but non-binding (“KR12–”) in <i>GUSB</i>; windows centered around a KR12 site (black arrow, dashed line) are within –500 to +500 bp; blue and orange arrows indicate cumulative coverage for the pulldown and input tracks, respectively. (C) Semi-quantitative PCR of <i>RPS18</i>, <i>KRAS</i>, <i>PIK3CA</i> and <i>GUSB</i> in the presence of 500 nM KR12 or DMSO as control. “Motif match” and “binding” indicate whether a particular gene contains a computationally predetermined match to the KR12 motif in the hg19 genome or a KR12 binding site determined by sequencing analysis, respectively.</p

Genome-wide effect of KR12 binding and implications of mutant codon 12 <i>KRAS</i> as a driver gene.

<p>(A) Mean expressions (vertical axis,–log₂FC) from RNA microarray analysis. Left: genome-wide KR12 binding (KR12-bound ‘+’, black; otherwise ‘–’, gray); middle: genes with computationally predetermined motif matches (‘+’) and those without (‘–’); right: expressions of genes with identified sites (‘+’) compared to genes with motif matches but no binding (‘–’) as determined by the workflow. <i>**</i>, <i>p</i> < .01 from two-sample Welch’s <i>t</i>-test; error bars indicate ±1 SEM. (B) Mean expressions (–log₂FC) of identified KR12-bound genes (“Post-validation”) compared to candidate genes following sliding-window determination (“Pre-validation”); “Difference” indicates pre-validation candidates not found in the Post-validation group. Error bars, ±1 SEM; <i>**</i>, <i>p</i> < .01 from two-sample Welch’s <i>t</i>-test. (C) Interaction network of down-regulated KR12-bound genes. <i>KRAS</i> (black) and its first neighbors (blue, marked with green arrows) are linked by solid black edges. Blue dashed edges indicate direct interactions with first neighbors of <i>KRAS</i>.</p

Chromatin accessibility of KR12.

<p>(A) Position-coverage plot of KR12 binding (9 bp per point, black and red) in relation to DHS regions (10,000 bp per point, gray) per chromosome. Horizontal axes, relative position along chromosome; vertical axes, relative coverage of a feature; for DHS regions, a coverage of 100% indicates that all 10,000 bp of a genomic region have DHS, while for KR12 sites, black spots (0%) indicate that a particular site is outside the boundaries of a DHS region, in contrast to the red sites (> 0%). (B) Gene expressions (vertical,–log₂FC) as a function of KR12 site proximity (horizontal, 1000 bp) to the histone modification feature H3K27Ac. Spearman’s correlation coefficient (<i>ρ</i> = –0.171) suggests a weak correlation with histone modification. (C) Comparison of predicted binding site counts in coding regions (CDS) and in the hg19 genome for KR12 (red) against 100 randomly selected motifs (black, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165581#pone.0165581.s010" target="_blank">S4 Table</a>); horizontal axis, ratio of binding sites per motif/KR12 binding sites; vertical axis, ratio of binding sites in CDS per motif/KR12. Dashed line with slope of 1 (gray) is provided as reference.</p