Thesis (PhD) -- McMaster University, 1997. / Also available via World Wide Web.

Thesis (Ph.D.)--Flinders University, School of Chemistry, Physics and Earth Sciences. / Typescript bound. Includes bibliographical references and list of publications. Also available online.

Thesis (Ph. D.)--Materials Science and Engineering, Georgia Institute of Technology, 2008. / Committee Chair: Sandhage, Kenneth; Committee Co-Chair: Kröger, Nils; Committee Co-Chair: Naik, Rajesh; Committee Member: Hud, Nicholas; Committee Member: Marder, Seth.

Thesis (Ph. D.)--University of California, Riverside, 2009. / Vita. Includes abstract. Includes bibliographical references (leaves 148-155). Issued in print and online. Available via ProQuest Digital Dissertations.

Le développement d'un nouveau médicament est un processus long et coûteux. Entre la détermination d'une cible thérapeutique et la mise sur le marché d'un nouveau médicament, plus de dix ans de recherche sont nécessaires pour un coût supérieur à un milliard d'euros.L'accélération de ce processus et la réduction de son coût restent un enjeu majeur. Pour y parvenir, les simulations numériques, peu coûteuses et rapides, sont massivement utilisées. Malgré cela, elles restent limitées, en partie à cause de la quantité très importante de molécules de solvant à considérer. La théorie de la fonctionnelle de la densité moléculaire permet d'étudier la solvatation de composés de n'importe quelle taille et de n'importe quelle forme. Elle prédit en quelques secondes seulement à la fois l'énergie libre de solvatation et une carte détaillée de la densité d'équilibre autour de ce soluté. Ces grandeurs étant à la base de nombreux autres calculs utilisés par l'industrie pharmaceutique, la MDFT ouvre donc une autre voie d'optimisation de ces process. Cette thèse consiste à effectuer le premier pas vers l'ensemble de ces applications. Pour cela, nous avons adapté la théorie ainsi que le code associé avant de l'appliquer à des systèmes biologiques. / Drug development is time and cost-consuming: It takes in average 10 years and 1 billion euros to move from a therapeutic target to a new drug. To speed up this process and reduce its cost, numerical simulation are massively used. Nevertheless, they remain limited, one reason of which is the huge amount of solvent molecules to consider. The molecular density functional theory is a liquid state theory that allows the study of the solvation thermodynamics of solutes of arbitrary shape. MDFT predicts, in few seconds only, the free energy of solvation and the solvent profils. These parameters are at the heart of many others calculation used by the pharmaceutical industry. This thesis is the first step towards these applications. For that purpose, we adapted the theory as well as the associated code to this new target, then applied them to system of biological interest.

La poursuite de nouveaux angles de recherche est depuis toujours l'un des facteurs clés du progrès scientifique. Au travers de ce travail, nous amenons de nouveaux éléments permettant d'ouvrir une discussion sur la dynamique moléculaire et la structure des biomolécules, étudiées par diffusion neutronique sous haute pression. Le projet d'étude s'axe sur différents sujets ayant pour dénominateur commun la haute pression en biologie, fil conducteur de ces recherches. L'intérêt de la haute pression en biologie n'est pas a priori évident ; pourtant, un grand nombre de points stimulent ce champ d'investigation. Une partie conséquente de la biosphère subit un environnement sous haute pression : les organismes barophiles des grands fonds marins subissent des conditions de stress uniques, qui soulèvent des questions sur l'adaptation biologique. D'autre part, la haute pression trouve un intérêt concret dans l'agro-alimentaire pour la conservation alimentaire ou, nouvellement, la fabrication de vaccins. Cependant, ces recherches se situent en aval des travaux qui nous intéressent dans cet ouvrage. La thèse présentée donne une vision plus théorique, ou phénoménologique, de processus tels que des états métastables protéiques, leur dénaturation, ou encore l'étude de la transition dynamique, aux travers d'expériences adaptées au besoin du sujet entrepris. Un tel travail ne permet pas de couvrir toutes les informations nécessaires pour aborder une vision globale du sujet. L'ouvrage se concentre donc sur l'étude par diffusion neutronique des effets de la pression en biophysique pour élaborer de nouvelles possibilités de recherches, qui seront discutées ici. / Seeking new research options have always been the heart of scientific progress. Through this work, new elements are brought to start a discussion about molecular dynamics and biomolecule structure studied through high pressure experiments with neutron scattering. The project explores different subjects all gathered around the high pressure guideline. High pressure interest in biology might seem quite opaque: however, a large amount of points justifies this investigation field. A large part of the biosphere undergoes high pressure stress due to the fact of its presence in the deep sea, raising question about biological adaptation to high pressure environment, for example. High pressure in the last decades has raised interest on other purposes like food conservation or vaccine fabrication. These research fields are on the final stage of the steps studied in this work, that starts its origin through more theoretical and phenomenological events. The manuscript covers different areas such as dynamical transition or metastable state and denaturation of proteins through experiments designed to the need of the research. Such a field requires a gigantic amount of investigation while restraining the possibilities of generalization. Thus, the work is focused on neutron scattering as a probe for high pressure studies in biophysics in order to elaborate new research clues in the field dealt with.

abstract: With the advent of the X-ray free-electron laser (XFEL), an opportunity has arisen to break the nexus between radiation dose and spatial resolution in diffractive imaging, by outrunning radiation damage altogether when using single X-ray pulses so brief that they terminate before atomic motion commences. This dissertation concerns the application of XFELs to biomolecular imaging in an effort to overcome the severe challenges associated with radiation damage and macroscopic protein crystal growth. The method of femtosecond protein nanocrystallography (fsPNX) is investigated, and a new method for extracting crystallographic structure factors is demonstrated on simulated data and on the first experimental fsPNX data obtained at an XFEL. Errors are assessed based on standard metrics familiar to the crystallography community. It is shown that resulting structure factors match the quality of those measured conventionally, at least to 9 angstrom resolution. A new method for ab-initio phasing of coherently-illuminated nanocrystals is then demonstrated on simulated data. The method of correlated fluctuation small-angle X-ray scattering (CFSAXS) is also investigated as an alternative route to biomolecular structure determination, without the use of crystals. It is demonstrated that, for a constrained two-dimensional geometry, a projection image of a single particle can be formed, ab-initio and without modeling parameters, from measured diffracted intensity correlations arising from disordered ensembles of identical particles illuminated simultaneously. The method is demonstrated experimentally, based on soft X-ray diffraction from disordered but identical nanoparticles, providing the first experimental proof-of-principle result. Finally, the fundamental limitations of CFSAXS is investigated through both theory and simulations. It is found that the signal-to-noise ratio (SNR) for CFSAXS data is essentially independent of the number of particles exposed in each diffraction pattern. The dependence of SNR on particle size and resolution is considered, and realistic estimates are made (with the inclusion of solvent scatter) of the SNR for protein solution scattering experiments utilizing an XFEL source. / Dissertation/Thesis / Ph.D. Physics 2011

This dissertation mainly focuses on analytical method development for characterization of proteins, glycoproteins and glycans using the recently developed ion mobility spectrometry (IMS) techniques and various electron activated dissociation (ExD) tandem mass spectrometry methods. IMS and ExD have become important techniques in structure analysis of biomolecules. IMS is a gas-phase separation method orthogonal to liquid chromatography (LC) fractionation. ExD is capable of producing a large number of structurally informative fragment ions for elucidation of structural details, complementary to collision-induced dissociation (CID). We first applied the selected accumulation-trapped IMS (SA-TIMS)-electronic excitation dissociation (EED) method to analyze various mixtures of glycan isomers. Glycan linkage isomers with linear or branched structure were successfully separated and subsequently identified. Theoretical modeling was also performed to gain a better understanding of isomer separation. The calculated collisional cross section (CCS) values match well with the experimentally measured ones, and suggested that the choice of metal charge carrier and charge state is critical for successful IMS separation of isomeric glycans. In addition, a SA-TIMS-electron capture dissociation (ECD) approach was employed to study gas-phase protein conformation, as the ECD fragmentation pattern is influenced by both the charge distribution and the presence of various non-covalent interactions. We demonstrated that different conformations of protein ions in a single charge state could produce distinct fragmentation pattern, presumably because of their differences in tertiary structures and/or proton locations. The second part describes characterization of glycoproteins using LC-hot ECD. To improve the cleavage coverage of glycopeptides, hot ECD, a fragmentation method utilizing the irradiation of high-energy electrons, was optimized for both middle-down and bottom-up analyses of glycopeptides, including peptides with multiple glycosylation sites. Hot ECD was shown to be an effective fragmentation technique for sequencing of glycopeptides, even for ions in lower charge states. In addition, the online LC-hot ECD approach was applied to characterize extensively modified glycoproteins from biological sources in which all glycosylation sites could be unambiguously determined. This study expands the applications of IMS, CID and ExD to structural analysis of various biomolecules, and explores the analytical potential of combining them for investigation of complex biological systems, in particular, enzyme mechanisms.

Dans cette thèse, nous avons développé et caractérisé un nouveau type de source de mise en phase gazeuse de biomolécules qui repose sur une désorption laser non résonnante sur des microgouttelettes directement sous vide. Ce dispositif nous permettra à terme d’ouvrir une voie d’étude originale pour appréhender les effets des rayonnements ionisants sur des molécules organiques d'un point de vue physique.Nous présenterons en détail ce dispositif avec lequel nous avons réussi à transférer sous vide, de façon non destructive, des biomolécules et des complexes non-covalents dans une gamme de masse de l’ordre du kDa et à les identifier par spectrométrie de masse par temps de vol. Nous montrerons notamment les défis techniques qu’il a fallu relever pour permettre le transfert des microgouttelettes sous vide et comment par simulation du spectromètre, nous sommes parvenus à optimiser fortement les paramètres de collection des espèces moléculaires désorbées et la résolution en masse de notre système, en remplaçant, dans la zone de désorption, l’extraction électrostatique à potentiels retardés par un piège électrostatique quadripolaire. Nous exposerons enfin la façon dont ce dispositif, couplé à une plateforme d'irradiation d'ions simplement chargés possédant une énergie de l'ordre du keV, nous permettra de caractériser à une échelle moléculaire l’endommagement lié à des mécanismes de chimie radicalaire radio-induits. / In this thesis, we have developed and characterized a new type of gas phase source of biomolecules which based on non-resonant laser desorption on microdroplets directly under vacuum. This device will eventually allow us to open an original way to study the effects of ionizing radiation on organic molecules from a physical point of view. We will present in detail this device with which we transfered with sucess under vacuum,in a non-destructively way, biomolecules and non-covalent complexes in a mass range of the order of kDa and we assigned them with time-of-ight mass spectrometry. We will show in particular the technical challenges that we had to overcome in order to allow the transfer of microdroplets under vacuum and how by simulation of the spectrometer, we have been able to highly optimize the collection parameters of the desorbed molecular species and the mass resolution of our system, by replacing, in the desorption zone,delayed extraction by a quadrupole electrostatic trap. Finally, we will describe the way in which this device, coupled to a simply charged ion irradiation platform with an energy of the order of the keV, will enable us to characterizeon a molecular scale the damage due to radio-induced radical chemistry mechanisms.

This study concerns halogen bonding between small molecules. Except where otherwise stated herein this investigation was performed exclusively using the M06-2X density functional, in conjunction with the 6-31+G* basis set except for iodine and astatine which were treated using the aug-cc-pVDZ-PP basis set with relativistic pseudopotentials. All calculations were performed in the gas phase. The counterpoise procedure was employed for all full geometry optimisations. Statistical analysis of the Cambridge Structural Database, wherein the frequency of structures as a function of halogen bond angle and distance constituted the sole part of this study not to be based on density functional theory. Except in chapter 5, all halogens from fluorine to astatine are investigated. In chapter 3, halogen bonding between halobenzene and a single water molecule is discussed. Competition between R – X•••OH2 halogen bonding and R – X•••H-O-H hydrogen bonding interactions is described. This system is analogous to the more elaborate microsolvated 1- methyl-5-halouracil system described in chapter 4. In this latter system one 1-methyl-5- halouracil molecule interacts with either one or two water molecules. A central feature of the investigation into this system is competition between R – X•••OH2 and R=O•••H-O-H hydrogen bonding. In chapter 5, halogen bonding is discussed in the context of the thyroid system. In particular halogen bonding between a thyroxine iodine atom and the protein backbone as well as crystal water molecules is the subject of this chapter. The effect of substitution of the iodine atom with an astatine atom is presented. Chapter 6 is concerned with halogen bonding in halogenated DNA base pairs. Interaction energies are compared with those of the canonical base pairs, and the effect of halogen bonding on geometry is also discussed. For each system, halogen bonding was found to become stronger and more tolerant of non- linear bond angles going down the halogen group.