Hydrogen-Bonded Clusters: A Study of the Elusive Anisole-Ammonia and Anisole-Water 1:1 Complexes

The hydrogen bond is one of the most important and versatile interactions found in most subsets of chemistry and biology. This interaction is responsible for reactions and characteristic properties of the systems in thereof. This interaction is just one of several available non-covalent interactions that can occur and over the past several decades of molecular spectroscopy studies, the definition of the hydrogen bond has become broader compared to the “classic” definition. To accurately study the hydrogen-bonding in these systems can be quite challenging due to the size and complexity of the molecules involved, as well as the other interactions that may play a role. In order to study these interactions, model systems containing the isolated conditions for hydrogen bonding similar to their real-world counterparts have been of great use. By studying the strength, geometric orientation, and spectral features of these systems, these types of interactions are better understood. Of the model systems involved, those containing ammonia and water have been widely studied due to the critical role of the two solvents across all of chemistry, especially biochemistry. In the past few decades, the anisole-ammonia and anisole-water 1:1 complexes, two potential candidates for hydrogen bonding, have been studied. However, these studies have been mostly comprised of initial experimental investigations and low-level theoretical calculations. This leaves some ambiguity as to the exact strength and binding motifs of these complexes. The focus of this thesis is to identify the shortcomings of the recent literature and answer some of the remaining questions. The ground-state experimental binding energy for the anisole-ammonia complex is reported for the first time via 2-color-resonant 2-photon ionization (2CR2PI) spectroscopy. Through several high-level DFT calculations, the ground-state structure and binding energy are reported and compared to previous literature. Also, the same plethora of theoretical methods were used to explore the complex in the cation-radical state for the first time. Similarly, the same theoretical investigations were employed to study the ground-state and cation radical structure and binding energy were studied for the anisole-water 1:1 complex. The results obtained were then compared to the previous studies

Strength of π-Stacking, from Neutral to Cation: Precision Measurement of Binding Energies in an Isolated π-Stacked Dimer

π-Stacking interactions are ubiquitious across chemistry and biochemistry, impacting areas from organic materials and photovoltaics to biochemistry and DNA. However, experimental data is lacking regarding the strength of π-stacking forces—an issue not settled even for the simplest model system, the isolated benzene dimer. Here, we use two-color appearance potential measurements to determine the binding energies of the isolated, π-stacked dimer of fluorene (C13H10) in ground, excited, and ionic states. Our measurements provide the first precise values for π-stacking interaction energies in these states, which are key benchmarks for theory. Indeed, theoretical predictions using ab initio and carefully benchmarked DFT methods are in excellent agreement with experiment

The Role of Torsional Dynamics on Hole and Exciton Stabilization in π‐Stacked Assemblies: Design of Rigid Torsionomers of a Cofacial Bifluorene

Exciton and charge delocalization across π‐stacked assemblies is of importance in biological systems and functional polymeric materials. To examine the requirements for exciton and hole stabilization, cofacial bifluorene (F2) torsionomers were designed, synthesized, and characterized: unhindered (model) MeF2, sterically hindered tBuF2, and cyclophane‐like CF2, where fluorenes are locked in a perfect sandwich orientation via two methylene linkers. This set of bichromophores with varied torsional rigidity and orbital overlap shows that exciton stabilization requires a perfect sandwich‐like arrangement, as seen by strong excimeric‐like emission only in CF2 and MeF2. In contrast, hole delocalization is less geometrically restrictive and occurs even in sterically hindered tBuF2, as judged by 160 mV hole stabilization and a near‐IR band in the spectrum of its cation radical. These findings underscore the diverse requirements for charge and energy delocalization across π‐stacked assemblies

π-π stacking vs. C–H/π interaction: Excimer formation and charge resonance stabilization in van der Waals clusters of 9,9′-dimethylfluorene

Studies of exciton and hole stabilization in multichromophoric systems underpin our understanding of electron transfer and transport in materials and biomolecules. The simplest model systems are dimeric, and recently we compared the gas-phase spectroscopy and dynamics of van der Waals dimers of fluorene, 9-methylfluorene (MF), and 9,9′-dimethylfluorene (F1) to assess how sterically controlled facial encumbrance modulates the dynamics of excimer formation and charge resonance stabilization (CRS). Dimers of fluorene and MF show only excimer emission upon electronic excitation, and significant CRS as evidenced in a reduced ionization potential for the dimer relative the monomer. By contrast, the dimer of F1 shows no excimeric emission, rather structured emission from the locally excited state of a tilted (non π-stacked) dimer, evidencing the importance of C–H/π interactions and increased steric constraints that restrict a cofacial approach. In this work, we report our full results on van der Waals clusters of F1, using a combination of theory and experiments that include laser-induced fluorescence, mass-selected two-color resonant two-photon ionization spectroscopy, and two-color appearance potential measurements. We use the latter to derive the binding energies of the F1 dimer in ground, excited, and cation radical states. Our results are compared with van der Waals and covalently linked clusters of fluorene to assess both the relative strength of π-stacking and C–H/π interactions in polyaromatic assemblies and the role of π-stacking in excimer formation and CRS

C–H/π and C–H–O Interactions in Concert: A Study of the Anisole–Methane Complex using Resonant Ionization and Velocity Mapped Ion Imaging

Noncovalent forces such as hydrogen bonding, halogen bonding, π–π stacking, and C–H/π and C–H/O interactions hold the key to such chemical processes as protein folding, molecular self-assembly, and drug–substrate interactions. Invaluable insight into the nature and strength of these forces continues to come from the study of isolated molecular clusters. In this work, we report on a study of the isolated anisole–methane complex, where both C–H/π and C–H/O interactions are possible, using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity mapped ion imaging (VMI). Using 2CAP and VMI, we derive the binding energies of the complex in ground, excited, and cation radical states. The experimental values from the two methods are in excellent agreement, and they are compared with selected theoretical values calculated using density functional theory and ab initio methods. The optimized ground-state cluster geometry, which is consistent with the experimental observations, shows methane sitting above the ring, interacting with anisole via both C–H/π and C–H/O interactions, and this dual mode of interaction is reflected in a larger ground-state binding energy as compared with the prototypical benzene–methane system

Chronic hand eczema in Europe:Patient experiences and perspectives (CHEPEP) in qualitative interviews

Background: Chronic hand eczema (CHE) is a very common skin disease among the European population. It causes itch and pain and, in more severe cases, seriously impairs hand functioning at work and in private life. Objectives: To explore perspectives of people with lived experience on CHE-related problems, wishes and goals. Methods: Following a qualitative approach, we conducted topic-guided interviews in five European countries and applied template analysis to identify recurrent themes among patients with CHE. Results: We interviewed 60 patients in seven outpatient dermatological and occupational medicine clinics in Croatia, Denmark, Germany, the Netherlands and Spain. Five main themes were identified: (1) knowledge about the disease and its course, (2) preventive behaviour, (3) hand eczema therapy, (4) impact on everyday life and (5) attitudes towards CHE and healthcare. Participants did not feel well informed about CHE, especially about causes, triggers and treatment options. Preventive measures were experienced as more or less effective but also cumbersome. Experiences with therapy were diverse. Treatment satisfaction depended on the results and on the perceived support from the treatment teams. Participants found it important to be taken seriously, to receive practical advice, to try out additional treatments or examinations, find new hope and have occupational perspectives. They wished that others could better understand the physical and emotional burden of CHE. Patient support groups were not mentioned. Participants found it important to learn to take care of themselves and accept life with CHE. Conclusions: Due to its annoying symptoms, high visibility and impaired functioning at work and in private life, CHE has a high emotional and social impact. Some people may require support to learn coping with CHE and its prevention. Patients wish for information about causes and triggers. They value physicians who listen to them and keep looking for solutions.</p

Nanopore native RNA sequencing of a human poly(A) transcriptome

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes

Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

SummaryGlobal dispersal and increasing frequency of the SARS-CoV-2 Spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of Spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large data set, well represented by both Spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the Spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.</jats:p

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic.

We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single-nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances, there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of 2 months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7's set of mutations.The COG-UK Consortium is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. O.G.P. was supported by the Oxford Martin School. J.T.M., R.M.C., N.J.L., and A.R. acknowledge the support of the Wellcome Trust (Collaborators Award 206298/Z/17/Z – ARTIC network). D.L.R. acknowledges the support of the MRC (MC_UU_12014/12) and the Wellcome Trust (220977/Z/20/Z). E.S. and A.R. are supported by the European Research Council (grant agreement no. 725422 – ReservoirDOCS). T.R.C. and N.J.L. acknowledge the support of the MRC, which provided the funding for the MRC CLIMB infrastructure used to analyze, store, and share the UK sequencing dataset (MR/L015080/1 and MR/T030062/1). The samples sequenced in Wales were sequenced partly using funding provided by the Welsh Government