AFRIKAANS: Rumohra adiantiformis (G. Forst.) Ching, die seweweeks- ofknysnavaring se gewildheid as loof in die snyblombedryf neem vinnig toe. Onder natuurlike groeitoestande ontwikkel die seweweeksvaring slegs beperkte hoeveelhede sori op blare, terwyl groot hoeveelhede sori ontwikkel wanneer die varing onder skadunet verbou word. Die teenwoordigheid van oormatige sori lei tot bemarkingsprobleme. Die navorsing is op die perseel van Bergland Tuine kwekery te Krugersdorp uitgevoer om die invloed van etefon, paklobutrasool (PP333), gibberelliensuur (GA3) , sitokiniene en verskillende skaduvlakke op sorivoorkoms en grootte van seweweeksvaringblare te bepaal. Behandeling van PP333 teen 500 mg dm-3 of met etefon teen 144 en 480 mg dm-3 in die blaarknopstadium het die getal sori by volwassenheid van blare betekenisvol verlaag. PP333-behandelings teen 1 000 en 1 500 mg dm-3 in die blaarknopstadium het die sori by volwassenheid van blare hoogs betekenisvol verlaag. Bespuitings met behandelings GA3 teen 57,6 mg dm-3 of sitokiniene teen 0,00062 en 0,0155 mg dm-3 op die blaarknopstadium het tot 'n betekenisvolle verhoging van sori op volwasse blare gelei. PP333 of etefon beinvloed nie die blaargrootte van volwasse blare wat in die jongblaar-, oopgevoudeblaar- en blaarknopstadium behandel is nie. Blare van al drie blaarstadia wat met sitokiniene of GA3 behandel is, was by volwassenheid nie-betekenisvol groter. Die 70% skadunet met bykomstige swartplastiekstroke in 'n noordsuidrigting onderaan gespan het die getal sori op blare verlaag en die blaaroppervlakte betekenisvol vergroot. Faktore soos seisoenale variasie, oesfrekwensie, plantdigtheid, grondvogstatus, waterkwaliteit, peste en plae was nie by hierdie ondersoek ingesluit nie en behoort ondersoek te word. ENGLISH: Rumohra adiantiformis (0. Forst.) Ching, the seven-weeks or knysna fern is a relatively new floral greenery of increasing importance. In its natural habitat the seven-weeks fern produces small numbers of sori on leaves, while commercially cultivated ferns under shade produce large numbers. The presence of excessive numbers of sori have a detrimental influence on the market value of the product. A trial was conducted on the premises of Bergland Tuine nursery in Krugersdorp to determine the effect of ethephon, paclobutrazol (PP333), gibberellic acid (GA3), cytokinins and different shade levels on the presence of sori and size of seven-weeks fern leaves. Leaves treated in the leafbud stage with PP333 at 500 mg dm-3 or ethephon at 144 and 480 mg dm-3 significantly reduced the number of sori on the leaves at maturity. Highly significant reduction of sori on mature leaves were found when PP333 was applied at I 000 and 1 500 mg dm-3 on the leaves in the leafbud stage. Sori numbers on mature leaves significantly increased after treatment of bud stage leaves with GA3 at 57,6 mg dm-3 or cytokinins at 0,00062 and 0,0155 mg dm-3. The leaf size of mature leaves was not influenced when PP333 or ethephon was applied on the leaves at the young leaf, unfolded leaf and leafbud stage. Leaves in all three leaf stages treated with cytokinins or GA3 showed a non-significant increase in leaf size at maturity. The 70% shade net with additional black plastic strips suspended underneath the net in a north-south direction, reduced the number of sori on the leaves and increased the leaf area significantly. Factors such as seasonal variation, harvest frequency, plant density, ground moisture levels, water quality, diseases and pests were not included in this investigation but should be researched. / Dissertation (MSc(Agric))--University of Pretoria, 2011. / Plant Production and Soil Science / unrestricted

This dissertation investigates Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) based techniques to study the impact of molecular structure on conformation and binding energetics. A novel method to determine collison cross sectional areas using FTICR (CRAFTI), initially developed by the Dearden lab, was applied to study the conformations of molecular systems with unique structural attributes in an attempt to explore the molecular range of CRAFTI. The systems chosen for CRAFTI studies include crown-ether alkylammonium complexes and biogenic amino acids. The results were found to be consistent with expected behavior, and strongly correlated with experimental measurements made using ion mobility spectrometry (IMS) and predictions from computations. The analytical sensitivity of CRAFTI was highlighted by its ability to distinguish the normal and branched structural isomers of butylamine. Besides conformation characterization, quantitative evaluation of binding was undertaken on metal ion-cryptand complexes on the FTICR instrument using sustained off-resonance irradiation-collision-induced dissociation (SORI CID) method. Complex formation and dissociation was found to be a strong function of both guest and host sizes which impacted steric selectivity, and polarizability. The results demonstrate the ability of FTICR to simultaneously determine structure, conformation and binding thereby providing comprehensive molecular characterization.

This thesis focuses on using mass spectrometry-based techniques for characterizing the structure and behavior of cucurbituril complexes in the gas phase. Both solvent and counter ion effects can be completely eliminated in the gas phase and the intrinsic interactions in the system are directly shown in the experimental results. Chapter 1 introduces the structures, properties and host-guest chemistry of cucurbituril, and FTICR mass spectrometry including instrumentation, performance and working principles. Two mass spectrometry-based methods for supramolecular characterization, sustained off-resonance irradiation collision induced dissociation (SORI CID) and ion molecule equilibrium measurements, are also discussed in this chapter. Chapter 2 characterizes the dissociation and reaction behaviors of the complexes formed by cucurbit[5]uril (CB5) and primary monoamines [CH3(CH2)nNH2, n = 0-7] as well as similar studies of decamethylcucurbit[5]uril (mc5) in the gas phase. This study probes host-guest interactions between the neutral cucurbituril host and alkyl chains of varying length. All the cucurbit[5]uril and decamethylcucurbit[5]uril complexes have external binding. The dissociation thresholds of the complexes suggest that the optimum monoammonium chain length for binding CB5 in the gas phase occurs for n = 2, whereas for mc5 the optimum is n = 0. Reactivity studies of CB5 and mc5 complexes indicate the highest binding affinity appears at n = 6 for CB5 and n = 5 for mc5. Chapter 3 investigates the complexes formed by cucurbit[6]uril and primary monoamines using energy resolved SORI CID methods and ion molecule equilibrium measurements. The fragmentation data, branching ratios for the various channels, and the reactivities of the complexes suggest the complexes have the monoammonium threaded through the cavity of CB6 forming a pseudorotaxane architecture. Reactivity studies of complexes of cucurbit[7]uril reveal behaviors distinctive from CB5, mc5 or CB6, which suggests both internally-bound and externally-bound structures are present in CB7 complexes.

In my dissertation, I use a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR-MS) to investigate supramolecules. Cross-sectional areas by Fourier transform ICR (CRAFTI), a novel technique for measurements of collision cross sections by FTICR, is demonstrated for the first time. The CRAFTI method measures the total "dephasing cross section" for removal of the ions from the coherent packet in the FTICR cell, including contributions not only from momentum transfer but also from reactive collisions including those leading to collisional dissociation. Experimental CRAFTI collision cross sections correlate linearly with theoretically computed results and with results obtained using ion mobility measurements. Different collision gases, including Xe, N2, Ar, and SF6, are all appropriate for the CRAFTI technique when the experiments are done at proper kinetic energies. The CRAFTI technique was applied to characterize the molecular shape of complexes of alkyl mono- and n-alkyldiamine with cucurbit[n]uril in the gas phase. The CRAFTI results are consistent with corresponding computational geometries. The CRAFTI technique was combined with SORI-CID (sustained off-resonance irradiation collision induced dissociation) for characterization of complexes of α,ω-alkyldiammonium with cucurbit[n]urils (n=5, 7 and 8) and cucurbituril derivatives. The results demonstrate that for bigger cucurbiturils, the complexes have the alkyldiamine tails threaded through the cavity of the host; for smaller cucurbiturils, the complexes have the tails of the alklydiamines external to the portal of the host.Capping molecules for larger CBn to form larger containers were also investigated. Using SORI-CID methods, CB7, a bigger cucurbituril cage, was found to form a more stable complex with Gu+ (guanidinium). Several neutral guests (benzene, fluorobenzene and toluene) were trapped in CB7 cavity to form inclusion complexes.

Presented in this dissertation are FT-ICR H/D exchange and fragmentation studies of protonated peptides for the purpose of better understanding gas phase conformation and protonation motifs, and their affect on fragmentation patterns. In addition, a new ion activation method is developed to enhance the abundance of higher energy fragmentation pathways, thereby providing additional structural and/or mechanistic information.Studies to probe the relay mechanism of H/D exchange in small, model peptides found that residue position, proline configuration, and availability of the termini have a measurable effect on the H/D exchange behavior reflective of different conformation / protonation motifs.Charge remote cleavage C-terminal to aspartic acid was studied with the fixed charge derivative tris(2,4,6-trimethoxyphenyl) phosphonium (tTMP-P+). Ab initio calculations demonstrate that tTMP-P+ cannot activate the proposed aspartic acid nucleophile, the acidic side chain hydrogen initiates cleavage. Despite the absence of an ionizing proton, the derivatized peptide P+LDIFSDF (where P+ = tTMP-P+) exchanges three acidic hydrogens for deuterium. This supports the proposed aspartic acid cleavage mechanism that occurs without the direct involvement of an ionizing proton because acidic protons are able to participate in H/D exchange in the absence of an added proton. In addition, H/D exchange of P+LDIFSDF analogues provides insight into the sites and mechanisms of H/D exchange.H/D exchange to separate distinct peptide populations with differing rates and their subsequent fragmentation demonstrate that conformation / protonation motif affects the fragmentation spectrum observed. Studies of [P+LDIFSDF + H]2+, [RPPGFSPFR + 2H]2+ (bradykinin), and [RVYIFPF + 2H]2+ show that at least two distinct structures exist with different rates of H/D exchange and different fragmentation patterns. The overall MS/MS spectrum is a linear combination of all conformations and protonation motifs. In addition, fragmentation of labeled populations suggests that complementary bn+ / ym-n+ ion pairs are being formed from doubly-charged precursor by the same mechanism.SORI-RE CID is a new FT-ICR ion activation method based on the combination of sustained off-resonance irradiation (SORI) and on-resonant excitation (RE) with the purpose of enhancing higher energy fragmentation while maintaining low energy processes. The experiments presented serve to illustrate the usefulness of SORI-RE in diverse cases.

This dissertation investigates non-covalent macromolecular chemistry using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) based techniques. The included studies reveal the impact of molecular structure on conformation and binding energetics. Supramolecules that might be too heavy to be dissociated in single collision-induced dissociation (CID) were dissociated using sustained off-resonance collision induced dissociation (SORI-CID) techniques. Relative binding energies and thresholds were evaluated for various macromolecular host-guest systems. Besides the non-covalent binding energies, conformation characterization was undertaken by a novel method to determine collision cross sectional areas using FTICR (CRAFTI, and multi-CRAFTI), initially developed by the Dearden lab. The systems chosen for further understanding of macromolecular interactions include calixarene-alkali metal complexes, cucurbit[5]uril-alkali halide complexes and cryptand-alkali metal complexes. The results were found to be consistent with expected behavior, and strongly correlated with predictions from computations. Size- and shape selectivity, as well as host-guest polarizability, are the main factors that govern the non-covalent macromolecular interactions that control complex conformation and dissociation. The results demonstrate the ability of FTICR to simultaneously determine binding energy, structure and conformation, which are the most important aspects for determination of comprehensive molecular characterization.

This dissertation expounds on the investigations of the structure and chemistry of peptides and supramolecular host-guest systems in the gas phase. These investigations used two different kinds of analytical instrument: Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and ion mobility mass spectrometry (IM-MS, IMS). These investigations were complemented by chemical modeling. The FTICR was used to radially trap ions with its 4.7 T magnet, which allowed the ions to undergo sustained off-resonance irradiation collision-induced dissociation (SORI-CID). A subsequent event then measured the collision cross sections (σ) of the targeted precursor ion and one of the selected product ions. These experiments were repeated multiple times to measure σ for as many precursor/product pairs as possible. A similar kind of experiment was performed in the IM-MS instrument, through in-source collision-induced dissociation and size-based ion separation in the instrument’s mobility region. When the precursor/product σ ratios were compared, the values obtained by both methods were in good agreement with each other. Application of the FTICR-based technique to [2.2.2]-cryptand+Cs+ caused the externally bound Cs+ to migrate into the cryptand’s cavity. Further development of the FTICR-based technique allowed me to perform the post-SORI σ measurements in a time-resolved fashion. Data collected in this manner revealed that collisionally activated peptides refold over a 5 – 10 second timescale, as determined by their σ shrinking with time. These experiments allowed for observation of a peptide refolding. The IM-MS instrument was applied to a supramolecular chemistry problem surrounding cucurbit[7]uril (CB7), and its ability to bind two identical guests within its cavity. Literature precedent and conventional wisdom suggested that only one guest would bind within CB7’s cavity while the other guest would be bound externally. When ion mobility cross sections (Ω) were obtained for [CB7 + Guest2]2+ systems, it was discovered that both guests could be bound within CB7’s cavity. This was possible because the guests possessed the correct shape and chemistry to favor dispersive interactions between CB7’s cavity and the adjacent guest, and ion-dipole interactions with CB7’s carbonyl-lined portal.

This dissertation focuses on the investigation of gas-phase characteristics of cucurbituril host-guest systems using ion mobility spectrometry (IMS) and related techniques. Collision cross-sections (CCS) of alkylammonium complexes of cucurbit[n]uril (CB[n]) are measured to understand the allosteric interactions that induce conformational changes in the complex in the presence of metal cations on one of the portals of the cucurbit[6]uril (CB[6]) host. Cationic species on one CB[6] rim sterically force longer linear alkylammonium guests out of the cucurbituril cavity during complex formation. Similarly, rigid cucurbituril-metal complexes were studied using IMS to demonstrate the effect of long-range ion-neutral interactions on the gas phase mobility of ions. The contributions of charge state and charge distribution to the ion mobility CCS measured using a drift tube ion mobility spectrometer (DTIMS) were studied. This IMS method characterization will help in the study of biomolecules and may answer some of the questions regarding CCS measurements in protein structures, that are still being debated. While most of the studies were done using an IMS system, this dissertation also includes gas phase characterization studies done using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. A novel gas-phase CCS measurement technique - cross sectional areas using Fourier transform ion cyclotron resonance mass spectrometry (CRAFTI) was attempted on bigger systems like the [cucurbit[6]uril-n-alkylammonium]+ complexes. Infrared multi-photon dissociation (IRMPD), collision induced dissociation (CID), and sustained off-resonance irradiation (SORI) studies were done on many CB[n] systems, which helped to extract useful structural information about the complexes.

No description available.

L'objectif de ma thèse est d'étudier des oligonucléotides et mononucléotides par de nouvelles techniques de fragmentation comme l'EDD (Electron-Detachment-Dissociation) et l'EID (Electron-Induced-Dissociation) qui font intervenir un bombardement d'électrons. Les échantillons sont d'abord ionisés par une source electrospray (ESI) qui permet une ionisation douce. Au cours de mon travail de thèse, je me suis intéressé à l'étude de petits oligonucléotides (ADN et ARN simples brins) et de mononucléotides par EDD et EID. Tout d'abord nous optimisons les différents paramètres qui ont permis d'obtenir en ESI les espèces multichargées pour étudier les processus EDD, EID d'oligonucléotides à des états de charge différents, afin d'obtenir le maximum d'ions fragments. Ces spectres seront comparés avec les spectres SORI-CID (Collision-Induced-Dissociation) et IRMPD (Infrared-Multiphoton-Dissociation) pour mettre en évidence les spécificités de l'EDD et EID par rapport au SORI-CID. Les spectres EDD et EID montrent quelques ions fragments qui ne sont pas observés dans les spectres SORI-CID et IRMPD parce que ces derniers ne conduisent pas aux ions radicalaires. Grâce aux ions fragments radicalaires obtenus en EDD et en EID, nous avons pu accéder au séquençage d'oligonucléotides riches en thymine pour lesquels il est difficile d'obtenir des informations par les méthodes conventionnelles. Enfin nous avons utilisé des techniques particulières de la technologie ICR et qui seront présentées dans ce manuscrit