Red-emitting organic fluorophores

PhD ThesisOur understanding of molecular photophysics has developed over the course of the twentieth and early twenty-first century. Mastering the underlying mechanisms of fluorescence from organic dyes necessitates development of many spectroscopic techniques. For a time the field was driven by studying increasingly elaborate molecular structures, but now attention has returned to smaller systems, even single chromophore entities. This has in part been influenced by cost, and many small chromophores for commercial use are being designed with very specific properties based on classic photophysics concepts. Even relatively small organic fluorophores display subtleties which can be influenced by minor changes in structure or local environment. As is observed in this work, there are cases where manipulation of a single atom can afford a major change in optical properties. Having understood the nature of absorption and emission, our attention turns to how this knowledge could be applied to understand intricate processes such as energy and electron transfer. Consequently it becomes possible to rationally design dyes with desirable properties, and new technologies emerge as a result. A prime example lies in recent efforts to enhance the efficiency of organic solar cells, where investigators have turned to exploiting E-type delayed fluorescence (a concept introduced decades earlier). Now the field is awash with applications where old principles have been utilized to the advantage of new technologies. This thesis is concerned with the particular problems of analyzing organic dyes which absorb and emit in the red region. The introductory chapter outlines how the molecular photophysics has evolved over decades and defines key concepts in optical spectroscopy. We also examine two state-of-the-art techniques which rely on an understanding of fluorescence and electron transfer: namely super-resolution fluorescence microscopy and singlet-exciton fission. Finally, some consideration is given to how the field will likely manifest itself in the near future. An investigation into the origin of the red absorption/fluorescence characteristic to aza-BODIPY dyes, a variant on the popular boron dipyrromethene (BODIPY) dye family, is the ii basis of Chapter 3. Aza-BODPIY dyes have a carbon atom replaced by nitrogen at the meso site, causing a 100 nm red-shift relative to regular BODIPY. Careful analysis of the photophysics of aza-BODIPY, alongside a non-aza analogue, builds a picture of how this relatively large change in the excited state energy landscape is achieved with such a minor modification to the core structure. Chapter 4 explores the triplet-exited state properties of a popular red-emitting organic semiconductor chromophore, TIPS-pentacene. We discuss various mechanisms leading to quenching of fluorescence at the expense of enhancing intersystem crossing into the triplet manifold for TIPS-pentacene, which sees high triplet or fluorescence yields depending on the environment. TIPS-pentacene is widely used as the basis for singlet-exciton splitting dyes, where two triplets are formed from the singlet-excited state. This is therefore a pertinent example for explaining just how one can access the triplet state. In Chapters 5 and 6, we examine a new bridged pentacene bichromophore, which undergoes exciton multiplication by intramolecular singlet fission. Transient absorption spectroscopy suggests there is strong communication between pentacene moieties in the bichromophore, showing an unusually delocalized triplet state. This is contrary to many other singlet fission chromophores based on pentacene. The problem of how to accurately measure fluorescence quantum yields in the red spectral region is tackled in Chapter 7. The difficulties with measuring fluorescence in this region are highlighted and an alternative method for recording fluorescence yields, thermal blooming spectroscopy, reintroduced. A series of red-emitting cyanine dyes is proposed as new ratiometric fluorescence yield standards. This work has involved construction of a bespoke instrument for the task. In the final chapter, the mechanism of fluorescence “blinking” in the context of super-resolution fluorescence microscopy is studied. Using a combination of steady-state and time-resolved spectroscopic measurements in conjunction with advanced analysis of super-resolution microscope data allows for an interpretation of how such regular and reliable on/off fluorescence blinking is achieved with a popular commercial cyanine dye. Previously proposed mechanisms are tested extensively by optical characterization of the system. It is inferred that isomerization plays a role in switching between states

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 x 10(-8)) or suggestively genome wide (p < 2.3 x 10(-6)). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/ near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/ near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass

Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

A correction to this article has been published and is linked from the HTML version of this article