Tandem Mass Spectrometric and Ion Mobility Studies of Supramolecular Complexes

Synthetic supramolecular systems share many similarities with natural biological assemblies, especially when considering that the structure and guest binding are typically governed by non-covalent interactions. As such, the defining characteristic is that only comparably weak forces define the shape of a synthetic supramolecule or the tertiary structure of a protein, so that the resulting dynamic binding mode makes structure elucidation challenging. One of the major advances in recent analytical chemistry has been the development of ion mobility-mass spectrometry (IM-MS) to tackle the challenging problems faced in proteomics, glycomics, metabolomics, and lipidomics. By analogy, the prospects of applying IM-MS to supramolecules are bright and it is to be expected that unprecedented analytical insights into diverse systems such as host-guest complexes, molecular devices, self-assemblies and metallosupramolecular complexes will be obtained. The recurrent theme throughout this dissertation is that both structure (differentiation of diastereomers, photoisomers, mechanoisomers) and non-covalent interactions (hydrogen bonding, $TTF^{n+}/TTF^{n+}$-charge repulsion, dispersive interactions) can be investigated by a combination of the three methods of ion-mobility mass spectrometry (IM-MS), collision-induced dissociation (CID) and gas-phase H/D-exchange (GP-HDX). In the study of the gas-phase chiral recognition of crown-ether ammonium complexes, the importance of a single hydrogen bond for the enantiodifferentiation was revealed. Similarly, in an azobenzene model a hydrogen bonding interaction led to an increased stability of the (Z)-photoisomer. This surprising observation illustrates an important aspect, namely that there can be significant differences between the gas-phase and the solution environment. In the absence of solvent, both the stabilization of charged sites and the Coulomb repulsion of nearby charges are accentuated. In a way, the conundrum of supramolecular mass spectrometry revolves around the problem that ions are easily manipulated in the gas-phase where a high analytic resolution power is available, to then face the question if the obtained results still reflect the solution environment. Therefore, it is very convincing to see that in three of the five presented studies, the solution environment is reflected in a quantitative fashion: In the quantification of the enantiomeric excess (first study), the quantification of photoisomer content (second study), and the quantitative determination of equilibrium constants for redox-controlled dethreading (third study). Together with these five studies, and the detailed description in the subsequent chapters, I expect the treatment to be useful also from the practitioner's point of view. It is my hope that the performance, speed, and reliability with which measurements can be performed with modern instrumentation will make IM-MS a routine analytical tool in the repertoire of the working supramolecular chemist

Project Retrosight. Understanding the returns from cardiovascular and stroke research: Case Studies

Copyright @ 2011 RAND Europe. All rights reserved. The full text article is available via the link below.This project explores the impacts arising from cardiovascular and stroke research funded 15-20 years ago and attempts to draw out aspects of the research, researcher or environment that are associated with high or low impact. The project is a case study-based review of 29 cardiovascular and stroke research grants, funded in Australia, Canada and UK between 1989 and 1993. The case studies focused on the individual grants but considered the development of the investigators and ideas involved in the research projects from initiation to the present day. Grants were selected through a stratified random selection approach that aimed to include both high- and low-impact grants. The key messages are as follows: 1) The cases reveal that a large and diverse range of impacts arose from the 29 grants studied. 2) There are variations between the impacts derived from basic biomedical and clinical research. 3) There is no correlation between knowledge production and wider impacts 4) The majority of economic impacts identified come from a minority of projects. 5) We identified factors that appear to be associated with high and low impact. This report presents the key observations of the study and an overview of the methods involved. It has been written for funders of biomedical and health research and health services, health researchers, and policy makers in those fields. It will also be of interest to those involved in research and impact evaluation.This study was initiated with internal funding from RAND Europe and HERG, with continuing funding from the UK National Institute for Health Research, the Canadian Institutes of Health Research, the Heart and Stroke Foundation of Canada and the National Heart Foundation of Australia. The UK Stroke Association and the British Heart Foundation provided support in kind through access to their archives

Computational characterization of novel solar light-harvesting dyes and electronic-transfer system

Light-harvesting devices are of fundamental importance in solar energy conversion. By mimicking natural photosynthetic systems, artificial photosynthetic adaptations are usually based on using organic dyes and transition metal complexes as light-harvesting antennas. To this aim, donor-p-acceptor dyes are potentially used as antennas in dye sensitized solar cells (DSSCs). The advantages of organic dyes are their adjustable optical properties coupled with low production costs. Metal complexes, in particular ruthenium(II) polypyridine complexes, are widely studied because of their unique combination of chemical and physical properties. The present thesis is a theoretical investigation of the photophysical and photochemical properties of several light-harvesting antennas and photosensitisers. The first part of the thesis is devoted to study a series of donor-p-acceptor dyes, based on 4-methoxy-thiazole chromophores and ruthenium(II) polypyridine complexes with 4H-imidazole ligands. Quantum chemical and TDDFT methods have been applied to investigate photophysical properties of the dyes, special mention deserve the performed simulation of resonance Raman (RR) intensities. Based on the calculated RR spectra, protonation effects and the character of the involved excited states could be unraveled. Substitution as well as anchoring was found to be of substantial influence for the photophysical properties, such as excitation energies and excited states characters, of the ruthenium(II) complexes. To allow for applications of the dyes, as e.g. in DSSCs, knowledge of electron transfer (ET) processes occurring at the dye-semiconductor interface is necessary. Such processes can be studied by means of semi-classical Marcus theory. To this aim, a model system of a ruthenium(II) dye linked to a titanium dioxide cluster was constructed. Quantum mechanical/molecular mechanical simulations coupled with molecular dynamics have been performed in order to get the ET rate

3,4-Phenylenedioxythiophenes (PheDOTs) functionalized with electron-withdrawing groupsand their analogs for organic electronics. Remarkably efficient tuning the energy levels in flatconjugated polymers

A novel, facile and efficient one-pot, microwave-assisted method of synthesis allowing an access to a new series of 3,4-phenylenedioxythiophene derivatives with electron-withdrawing groups at the benzene ring (EWG-PheDOT) and their analogs (with an expanded side π-system or with heteroaromatic rings, ArDOT) by the reaction of 2,5-dialkoxycarbonyl-3,4-dihydroxythiophenes with electrophilic aromatic/heteroaromatic compounds in dipolar aprotic solvents has been described. Its applicability over a wide range of novel functionalized ArDOTs as promising building blocks for organic electronic materials has been demonstrated. The structures of selected ArDOTs have been determined by single-crystal X-ray diffraction. The electronic structure of conjugated polymers p[ArDOTs] based on synthesized novel thiophene monomers has been studied theoretically by the DFT PBC/B3LYP/6-31G(d) method. The performed calculations reveal that while the side functional groups are formally not in conjugation with the polymer main chain, they have an unprecedentedly strong effect on the HOMO/LUMO energy levels of conjugated polymers, allowing their efficient tuning by over the range of 1.6 eV. In contrast to that, the energy gaps of the polymers are almost unaffected by such functionalizations and vary within a range of only ≤0.05 eV. Computational predictions have been successfully confirmed in experiments: cyclic voltammetry shows a strong anodic shift of p-doping for the electron-withdrawing CF3 group functionalized polymer p[4CF3-PheDOT] relative to the unsubstituted p[PheDOT] polymer (by 0.55 V; DFT predicted the decrease of the HOMO by 0.58 eV), while very similar Vis-NIR absorption spectra for both polymers in the undoped state indicate that their optical energy gaps nearly coincide (ΔEg < 0.04 eV). © 2018 The Royal Society of Chemistry

Study on open science: The general state of the play in Open Science principles and practices at European life sciences institutes

Nowadays, open science is a hot topic on all levels and also is one of the priorities of the European Research Area. Components that are commonly associated with open science are open access, open data, open methodology, open source, open peer review, open science policies and citizen science. Open science may a great potential to connect and influence the practices of researchers, funding institutions and the public. In this paper, we evaluate the level of openness based on public surveys at four European life sciences institute

Time-dependent metabolic phenotyping of inflammatory dysregulation

A rich and functional description of a patient health status is the fundamental basis for the personalisation of treatment and the targeting of interventions. The function of inflammation in the healing process as well as its involvement in most major diseases is well established, yet the specific mechanism by which it contributes to the pathogenesis is still not fully understood. If conditions arising from a dysregulation of the inflammatory process are to be treated before they become irreversible, a novel understanding of these pathologies must be achieved and a stratification of patients based on their inflammatory status undertaken. The work presented in this thesis aims to deliver new analytical and statistical approaches to support the investigation of the time-dependent dysregulation of inflammation. Lipid mediators have been described as exerting a major role in the initiation and regulation of the inflammatory response, yet analytical platforms for their large-scale characterisation in human biofluids are lacking. This thesis reports the validation of an assay for the simultaneous quantification of pro- and anti-inflammatory signalling molecules in multiple human biofluids. The coverage of the assay in each biofluid is subsequently established, characterising inflammatory signalling across biological compartments. A second study explores the assay’s applicability in a clinical context; investigating the relationship between lipid mediators, current clinical markers of inflammation and post-operative complications. Characterising the interplay between signalling and regulatory networks is key to understanding a living system’s response to perturbations, yet few statistical approaches are suited for the detection of time-dependent patterns in short and irregularly sampled longitudinal datasets. This thesis reports the development of a statistical approach to support the identification of altered time-trajectories in such studies. The method’s wide applicability is subsequently demonstrated on two investigations covering the diversity of metabolic phenotyping data generation platforms. This thesis is a proof of concept for the characterisation of patient-specific inflammatory status in a clinical context and the identification of altered time-dependent patterns. Both analytical and statistical developments have been motivated by the needs of real world applications and provide a template for the characterisation and analysis of the molecular basis for treatment.Open Acces

Pharmacokinetics and biotransformation of biopharmaceuticals:by liquid chromatography with unit-mass and high-resolution mass spectrometric detection

Unlike the current situation for small-molecule drugs, the biotransformation of biopharmaceuticals is a largely unexplored field. Although much attention is paid to (the prevention of) degradation and structural alteration of protein-based drugs in pharmaceutical formulations, almost nothing is known about what happens to such a drug once it is dosed to a patient. An important reason for this is the fact that it is virtually impossible to investigate biotransformation using LBAs, because they typically cannot distinguish unchanged and biotransformed versions of the drug. With the increasing use of LC-MS/MS for protein quantification, it is now becoming more and more evident that in vivo chemical and enzymatic reactions of biopharmaceuticals are very common. Pharmacologically, biotransformation may affect the activity of a protein drug and, from an analytical perspective, it can also have a large influence on the concentration result that is reported.If we look at biopharmaceutical analysis from a more technical and instrumental point of view. So far, most protein LC-MS methods are being performed using triple-quadrupole mass spectrometry after sample digestion and further sample processing. This type of mass spectrometry has unit-mass resolution and its use for protein quantification essentially is an extension of the typical approach for small-molecule analysis. Very little is known about the quantitative possibilities of other high-resolution mass spectrometry (HRMS) approaches for biopharmaceuticals. HRMS is extensively used for qualitative purposes, such as the structural elucidation or confirmation of both small and large molecules, because of its high mass accuracy, but it also offers the option for quantitative analysis and extensive data re-processing. It can thus be used as an alternative detection technique for digested protein analysis with improved selectivity compared to unit-mass MS and it also is capable of quantifying intact proteins, which is virtually impossible on triple-quadrupole instrumentation

More is Different: Modern Computational Modeling for Heterogeneous Catalysis

La combinació d'observacions experimentals i estudis de la Density Functional Theory (DFT) és un dels pilars de la investigació química moderna. Atès que permeten recopilar informació física addicional d'un sistema químic, difícilment accessible a través de l'entorn experimental, aquests estudis es fan servir àmpliament per modelar i predir el comportament d'una gran varietat de compostos químics en entorns únics. A la catàlisi heterogènia, els models DFT s'utilitzen habitualment per avaluar la interacció entre els compostos moleculars i els catalitzadors, vinculant aquestes interpretacions amb els resultats experimentals. Tanmateix, l'alta complexitat trobada tant als escenaris catalítics com a la reactivitat, implica la necessitat de metodologies sofisticades que requereixen automatització, emmagatzematge i anàlisi per estudiar correctament aquests sistemes. Aquest treball presenta el desenvolupament i la combinació de múltiples metodologies per avaluar correctament la complexitat d'aquests sistemes químics. A més, aquest treball mostra com s'han utilitzat les tècniques proporcionades per estudiar noves configuracions catalítiques d'interès acadèmic i industrial.La combinación de observaciones experimentales y estudios de la Density Functional Theory (DFT) es uno de los pilares de la investigación química moderna. Dado que permiten recopilar información física adicional de un sistema químico, difícilmente accesible a través del entorno experimental, estos estudios se emplean ampliamente para modelar y predecir el comportamiento de una gran variedad de compuestos químicos en entornos únicos. En la catálisis heterogénea, los modelos DFT se emplean habitualmente para evaluar la interacción entre los compuestos moleculares y los catalizadores, vinculando estas interpretaciones con los resultados experimentales. Sin embargo, la alta complejidad encontrada tanto en los escenarios catalíticos como en la reactividad, implica la necesidad de metodologías sofisticadas que requieren de automatización, almacenamiento y análisis para estudiar correctamente estos sistemas. Este trabajo presenta el desarrollo y la combinación de múltiples metodologías con el objetivo de evaluar correctamente la complejidad de estos sistemas químicos. Además, este trabajo muestra cómo las técnicas proporcionadas se han utilizado para estudiar nuevas configuraciones catalíticas de interés académico e industrial.The combination of Experimental observations and Density Functional Theory studies is one of the pillars of modern chemical research. As they enable the collection of additional physical information of a chemical system, hardly accessible via the experimental setting, Density Functional Theory studies are widely employed to model and predict the behavior of a diverse variety of chemical compounds under unique environments. Particularly, in heterogeneous catalysis, Density Functional Theory models are commonly employed to evaluate the interaction between molecular compounds and catalysts, lately linking these interpretations with experimental results. However, high complexity found in both, catalytic settings and reactivity, implies the need of sophisticated methodologies involving automation, storage and analysis to correctly study these systems. Here, I present the development and combination of multiple methodologies, aiming at correctly asses complexity. Also, this work shows how the provided techniques have been actively used to study novel catalytic settings of academic and industrial interest

Thermal non-equilibria promote prebiotic DNA and RNA polymerization

Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of monomer building blocks are required. Before compartmentalization occurred on early Earth, prebiotic de novo strand formation of nucleic acids suffered from dilution of reagents and products. In this doctoral thesis, I show that the ubiquitous non-equilibrium conditions within heated underwater rock cracks on early Earth could have formed a natural habitat for nurturing RNA and DNA polymerization. This study demonstrates how the yield of otherwise inefficient primordial polymerization reactions is enhanced by a physical non-equilibrium triggered by thermal gradients. Heat fluxes across a thin rock crack accumulate the monomeric building blocks of DNA and RNA which enhances their polymerization. Also the resulting polymers are localized inside the pore over long times and protected against diffusion. Enclosed gas bubbles can additionally trigger micro-scale wet-dry cycles and enable dry-based reaction. In a closed system, I found nucleotides concentrate 10-fold at the bottom of the lab-built crack after 24 hours with a $10^4$-fold relative accumulation for the chosen \SI{40}{\milli\metre} high crack. I found enhanced polymerization from aminoimidazolized DNA nucleotides and 2',3'-cyclic RNA nucleotides, up to 25-fold. The activity of these substrates is known to be very limited under isothermal bulk conditions. Moreover, co-polymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal trap showed an increased heterogeneity in sequence composition compared to isothermal drying, enlarging the encoded sequence space. Finite element simulations on long time-scales showed how open pores with continuous collection of reagents can accommodate an active polymerization reaction over years while the escape of the nucleotides from the crack is negligible. This simple physical non-equilibrium habitat of a heated, water-filled rock pore creates an active, cell-like compartment that accumulates nucleotides for polymerization and traps RNA strands, providing a pre-cellular non-equilibrium setting for the first steps of molecular evolution.Das Leben basiert auf den Informationspolymeren DNA und RNA. Für ihre Polymerisation sind hohe Konzentrationen von initialen Monomerbausteinen erforderlich. Bevor es auf der frühen Erde zur Kompartimentierung kam, litt die präbiotische de novo Strangbildung von Nukleinsäuren unter der Verdünnung ihrer Edukte und Produkte. In dieser Doktorarbeit zeige ich, dass die allgegenwärtigen Nicht-Gleichgewichtsbedingungen in erhitzten Unterwasser-Gesteinsspalten auf der frühen Erde ein natürliches Habitat für eine erhöhte RNA- und DNA-Polymerisation gebildet haben können. Diese Studie zeigt, wie die Ausbeute von ansonsten ineffizienten primordialen Polymerisationsreaktionen durch ein physikalisches Nicht-Gleichgewicht, das durch thermische Gradienten angetrieben wird, erhöht wird. Wärmeströme durch dünne Gesteinsrisse akkumulieren die monomeren Bausteine von DNA und RNA, was deren Polymerisation fördert. Auch bleiben die entstehenden Polymere bleiben über lange Zeiten im Inneren der Pore lokalisiert und vor Diffusion geschützt. Eingeschlossene Gasblasen können zusätzlich mikroskopische Nass-Trocken-Zyklen auslösen und eine trockene Polymerisationsreaktion in einer wasserhaltigen Umwelt ermöglichen. In einem geschlossenen System wurde nach 24 Stunden eine 10-fache Aufkonzentration von Nukleotiden am Boden des im Labor nachgebauten Risses gefunden, mit einer $10^4$-fachen relativen Akkumulation für die gewählte \SI{40}{\milli\metre} hohe Pore. Eine bis zu 25-fach erhöhte Polymerisation von aminoimidazolisierten DNA-Nukleotiden und 2',3'-zyklischen RNA-Nukleotiden konnte nachgewiesen werden. Es ist bekannt, dass die Aktivität dieser Substrate unter normalen, isothermen Bedingungen im Bulk sehr begrenzt ist. Darüber hinaus zeigte die gemeinsame Polymerisation von 2',3'-cGMP und 2',3'-cCMP in der thermischen Falle eine erhöhte Heterogenität in der Sequenzzusammensetzung im Vergleich zur isothermen Trocknung, wodurch der kodierte Sequenzraum vergrößert wird. Finite-Elemente-Simulationen auf langen Zeitskalen zeigten, wie offene Poren mit kontinuierlicher Anreicherung von Reagenzien eine aktive Polymerisationsreaktion über Jahre hinweg beherbergen können, während das Entweichen der Oligonukleotide aus dem Riss vernachlässigbar war. Dieses einfache physikalische Nichtgleichgewichtshabitat einer geheizte, wassergefüllten Gesteinspore schafft ein aktives, zellähnliches Kompartiment, das Nukleotide für die Polymerisation akkumuliert und RNA- und DNA-Stränge zurückbehält, wodurch eine präzelluläre Nichtgleichgewichtsumgebung für die ersten Schritte der molekularen Evolution entsteht