Visible light-responsive photoswitches

The structure and properties of photochromic compounds can be altered with light. These photoswitches are ideally addressed with visible light. Various switching motifs are known, each with a different response to light. Donor-Acceptor Stenhouse Adducts (DASAs) re-emerged as visible light responsive photoswitches in 2014, and have already found numerous applications. These molecules can be isomerised with green light between a coloured linear form and a colourless cyclic form. One of the major limitations of these compounds was the range of solvents in which reversible isomerisation is possible. Reversible switching of the initially reported DASAs was only demonstrated in apolar solvents. With the work described in this thesis, isomerisation in a wide range in polar organic solvents is possible. The introduction of aniline-based DASAs, recognised as ‘second generation’ DASAs, led to reversible switching possible in chloroform and acetonitrile. However, the improved photocyclisation comes at the cost of the thermal equilibrium, and large fractions of the cyclic isomer remain present in the dark. Further advances towards switching in water have been made by altering the acceptor group and the first examples of reversible isomerisation in the polar solvents ethanol and DMSO are demonstrated. Establishing a structure-function relationship on ‘first generation’ DASAs has found minor changes in the structure can render these compounds excellent switches in common solvents such as chloroform. This work provides a guideline for the rational design of new compounds. The minor isomers found in solution have been identified and their role towards cyclisation has been studied. Although overlooked in the literature, these minor linear isomers could be part of an alternative path of isomerisation. In solution the cyclic isomer can be present as two tautomeric structures, depending on amine donor, solvent and concentration. For some applications the delicate difference between the two tautomers may have a significant effect on the functionality of the switch, and rational design of the DASA can vastly improve photoinduced changes

Genome-wide occupancy links Hoxa2 to Wnt–β-catenin signaling in mouse embryonic development

The regulation of gene expression is central to developmental programs and largely depends on the binding of sequence-specific transcription factors with cis-regulatory elements in the genome. Hox transcription factors specify the spatial coordinates of the body axis in all animals with bilateral symmetry, but a detailed knowledge of their molecular function in instructing cell fates is lacking. Here, we used chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) to identify Hoxa2 genomic locations in a time and space when it is actively instructing embryonic development in mouse. Our data reveals that Hoxa2 has large genome coverage and potentially regulates thousands of genes. Sequence analysis of Hoxa2-bound regions identifies high occurrence of two main classes of motifs, corresponding to Hox and Pbx–Hox recognition sequences. Examination of the binding targets of Hoxa2 faithfully captures the processes regulated by Hoxa2 during embryonic development; in addition, it uncovers a large cluster of potential targets involved in the Wnt-signaling pathway. In vivo examination of canonical Wnt–β-catenin signaling reveals activity specifically in Hoxa2 domain of expression, and this is undetectable in Hoxa2 mutant embryos. The comprehensive mapping of Hoxa2-binding sites provides a framework to study Hox regulatory networks in vertebrate developmental processes

Dielectric constant engineering of organic semiconductors: effect of planarity and conjugation length

Bulk heterojunction organic solar cells continue to show steady photoconversion efficiency improvements. However, single component organic solar cells are a particularly attractive alternative due to the relative simplicity of device manufacture. It has been proposed that organic semiconductors with a high dielectric constant (≈10) could give rise to spontaneous free charge carrier generation upon photoexcitation. In this manuscript, factors are explored that affect the dielectric constant of organic semiconductors, particularly the optical-frequency dielectric constant. The properties of monomers, dimers and trimers of two isoelectronic families of materials that have acceptor units composed of one or two dicyanovinylbenzothiadiazole moieties and one to three donor units are compared. The donor components are composed of either fluorenyl or cyclopentadithiophene moieties with the same glycol-based solubilizing groups. It is found that chromophore planarity and orientation with respect to the substrate, and film density affect the optical and electronic properties of the materials, especially the high-frequency dielectric constant. The results also indicate that delocalization of the highest occupied and lowest unoccupied molecular orbitals is a critical factor. The dimer with two dicyanovinylbenzothiadiazole moieties and two dithienocyclopentadiene units is found to have the highest optical frequency dielectric constant and overall performance

Dielectric constant engineering of organic semiconductors: effect of planarity and conjugation length

Bulk heterojunction organic solar cells continue to show steady photoconversion efficiency improvements. However, single component organic solar cells are a particularly attractive alternative due to the relative simplicity of device manufacture. It has been proposed that organic semiconductors with a high dielectric constant (≈10) could give rise to spontaneous free charge carrier generation upon photoexcitation. In this manuscript, factors are explored that affect the dielectric constant of organic semiconductors, particularly the optical-frequency dielectric constant. The properties of monomers, dimers and trimers of two isoelectronic families of materials that have acceptor units composed of one or two dicyanovinylbenzothiadiazole moieties and one to three donor units are compared. The donor components are composed of either fluorenyl or cyclopentadithiophene moieties with the same glycol-based solubilizing groups. It is found that chromophore planarity and orientation with respect to the substrate, and film density affect the optical and electronic properties of the materials, especially the high-frequency dielectric constant. The results also indicate that delocalization of the highest occupied and lowest unoccupied molecular orbitals is a critical factor. The dimer with two dicyanovinylbenzothiadiazole moieties and two dithienocyclopentadiene units is found to have the highest optical frequency dielectric constant and overall performance

Anion binding affinity: acidity versus conformational effects

High-level quantum chemical calculations were used to elucidate the gas- and solution-phase conformational equilibria for a series of symmetrically substituted (thio)ureas, (thio)squaramides, and croconamides. Gas-phase calculations predict that the thermodynamic conformer of many of these anion receptors is not the dual-hydrogen-bond-facilitating anti-anti conformer as is commonly assumed. For ,'-diaryl thiosquaramides and croconamides, the syn-syn conformer is typically the predominant conformer. Solution-phase calculations show that the anti-anti conformer is increasingly stabilized as the polarity of the solvent increases. However, the syn-syn conformer remains the lowest energy conformation for croconamides. These predictions are used to explain the acidity versus chloride binding affinity correlations recently reported for some of these compounds. The chloride binding constants for thioureas and croconamides are significantly lower than expected on the basis of their p values, and this may be due in part to the need for these receptors to reorganize into the anti-anti conformer. Experimental NMR nuclear Overhauser effect (NOE) measurements of an asymmetrically substituted squaramide and its thio analogue are consistent with the syn-syn conformation being predominant at 298 K. The conformational equilibria should therefore be an important consideration for the design and development of future anion receptors and organocatalysts

Hydrogen‐bonding donor‐acceptor Stenhouse adducts

The binding of donor-acceptor Stenhouse adducts (DASAs) bearing hydrogenbond recognition groups by Hamilton-type receptors significantly influenced their photoswitching properties by altering thermal barriers to isomerization. The thermal barrier between the most stable linear isomer and the photo-generated isomer is lowered on binding to a receptor, and this barrier is crucial for switching properties. The thermal isomerization was shown to proceed via a stepwise linear-enol-keto mechanism in DMSO where the barrier to tautomerisation is within 2 kJ•mol-1 of that of the rate-determining step, which may be important for analyzing switching properties

Hydrogen‐bonding donor‐acceptor Stenhouse adducts

The binding of donor-acceptor Stenhouse adducts (DASAs) bearing hydrogenbond recognition groups by Hamilton-type receptors significantly influenced their photoswitching properties by altering thermal barriers to isomerization. The thermal barrier between the most stable linear isomer and the photo-generated isomer is lowered on binding to a receptor, and this barrier is crucial for switching properties. The thermal isomerization was shown to proceed via a stepwise linear-enol-keto mechanism in DMSO where the barrier to tautomerisation is within 2 kJ•mol-1 of that of the rate-determining step, which may be important for analyzing switching properties

Structure-function relationships of donor-acceptor Stenhouse adduct photochromic switches

The first in-depth, systematic study of the photoswitching properties of Donor-Acceptor Stenhouse Adducts (DASAs) is reported. Barbituric acid derived DASAs functionalised with 14 different amines ranging from dimethylamine to 4-methoxy-N-methylaniline were structurally characterised in solution using H and C NMR spectroscopy and, in eight cases, in the solid state by single crystal X-ray diffraction. The distribution of coloured and colourless isomers in the dark, their photostationary states under irradiation, apparent thermal half-lives, and fatigue resistance are systematically compared. A simple kinetic model is used to characterise photoswitching behaviour and reveals that minor structural modifications can significantly improve the photoswitching properties of DASA photochromes. These modifications result in excellent photoswitching properties for '1 generation' DASAs in chloroform, including exceptional fatigue resistance, opening the door for these photochromic molecules to find widespread applications

A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree

This deposit is composed by the main article plus the supplementary materials of the publication.Connection of the heart to the systemic circulation is a critical developmental event that requires selective preservation of embryonic vessels (aortic arches). However, why some aortic arches regress while others are incorporated into the mature aortic tree remains unclear. By microdissection and deep sequencing in mouse, we find that neural crest (NC) only differentiates into vascular smooth muscle cells (SMCs) around those aortic arches destined for survival and reorganization, and identify the transcription factor Gata6 as a crucial regulator of this process. Gata6 is expressed in SMCs and its target genes activation control SMC differentiation. Furthermore, Gata6 is sufficient to promote SMCs differentiation in vivo, and drive preservation of aortic arches that ought to regress. These findings identify Gata6-directed differentiation of NC to SMCs as an essential mechanism that specifies the aortic tree, and provide a new framework for how mutations in GATA6 lead to congenital heart disorders in humans.Medical Research Council grant: (MR/L009986/1); Biotechnology and Biological Sciences Research Council grant: (BB/N00907X/1); National Institute of Neurological Disorders and Stroke grant: (NS038183).info:eu-repo/semantics/publishedVersio

Photochromic switching behaviour of donor-acceptor Stenhouse adducts in organic solvents

We report photochromic donor-acceptor Stenhouse adducts (DASAs) capable of fully reversible photoisomerization with visible light in organic solvents including chloroform, acetonitrile and benzene. The rates of photoisomerization and thermal reversion can be tuned by altering the electronics of the donor adduct. X-Ray crystallography and photo-NMR experiments unambiguously establish molecular structures