Дисертації: "Molecular cation"

1

Chauhan, Seema. "Molecular physiology of intestinal organic cation transport." Thesis, University of Newcastle Upon Tyne, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246636.

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2

Bleasby, Kelly. "The molecular physiology of renal organic cation transport." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437555.

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3

Connorton, James. "Molecular and phenotypic characterisation of plant cation exchangers." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/molecular-and-phenotypic-characterisation-of-plant-cation-exchangers(8f464803-46a3-44ae-99db-22703a6fbcbe).html.

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The cation exchanger (CAX) proteins are an important six-membered family of Arabidopsis antiporters thought to provide metal tolerance and to be key components in resetting cytosolic Ca2+ levels following a signalling event. CAX1 and CAX3 in particular have been implicated in this role and are thought to functionally associate although the expression profiles of the two genes are distinct to shoot and root tissue respectively under most circumstances. Here the CAX1-CAX3 interaction is confirmed through in vivo bimolecular fluorescence complementation and shown to localise to the tonoplast. Furthermore the site of the interaction is partially mapped to an N-terminal region distinct from the previously-identified N-terminal regulatory region through studies of the molecular behaviour of split-protein constructs. The co-localisation of CAX1 and CAX3 is confirmed through fluorescent-protein tagged recombinant protein analysis and preliminary data suggesting an additional, nuclear location for CAX1 is presented. An 11-transmembrane domain model is given for the membrane topology of CAX1 based on combination of experimental analysis through partial proteolysis of tagged recombinant proteins and computer-based analysis. In addition the physiological significance of CAX1, CAX2 and CAX3 is examined through the analysis of single and double knockout mutant plants and a CAX1-overexpressor plant in response to metal stress. Previously unknown phenotypes with regard to metal sensitivities, germination profiles and stress-induced membrane permeability characteristics are identified and discussed. These studies are interpreted with a view to further establishing the relationship between the structure and regulation of the CAX proteins and their function.

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4

Britton, Mathew. "Isolating the gain in the nitrogen molecular cation." Thesis, Université d'Ottawa / University of Ottawa, 2020. http://hdl.handle.net/10393/41238.

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The nitrogen molecular cation is a promising gain medium for the air laser, which could be a powerful tool for remote sensing applications. After nearly a decade of international scientific effort, there are still questions about the gain mechanisms. This thesis explores gain in the nitrogen molecular ion using an experimental configuration that isolates the generation of gain from uncontrolled effects. We use a narrow nitrogen gas jet in vacuum to minimize propagation distance and a probe pulse to measure gain. We first test the role of inelastic scattering during electron recollision as a mechanism to populate the excited state, and we find that it has a small contribution. Then, we measure gain dynamics by varying the probe delay. We measure short- and long-term gain in different conditions. The long-term gain is consistent with the decay of population inversion due to collisions between electrons and ions in the plasma. The decay is modulated due to rotational wave packets in the states of the ion. Rotational coherence decays on the same timescale as the gain due to the incoherent mixing of states. We then introduce an additional non-ionizing pulse that interacts with the ion after ionization. The additional pulse changes the experiment to pump-probe spectroscopy on the ion itself. It can manipulate the rotational wave packets. It can also halt or redirect the emission following the probe pulse by coupling the ground lasing state with a middle state. In both cases, it controls the characteristics of gain and emission at a distance. These interactions highlight the role of the middle state, which is an essential ingredient for gain. Short-term gain appears at low pump intensity when the pump or control pulses overlap the probe pulse. It is consistent with wave mixing due to Raman gain in a V-system.

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5

Galamba, Joseph. "Model of the One-Dimensional Molecular Hydrogen Cation." Oberlin College Honors Theses / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=oberlin1337904721.

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6

Ryan, Jennifer Susan. "Molecular signaling pathways regulating cation channels in ocular epithelial cells." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape9/PQDD_0019/NQ49289.pdf.

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7

Hernandez-Alvarado, Edgardo Manuel. "Synthesis Of Porphyrin Containing Molecular Dyads For Radical-Cation Generation." Diss., The University of Arizona, 2014. http://hdl.handle.net/10150/338955.

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The overall efficiency of photovoltaics is dictated by processes occurring within it. These processes include exciton formation, diffusion, dissociation and charge collection. This dissertation will focus around the fundamental issue of charge collection. In organic photovoltaics (OPVs) the rate of charge injection is dominated by the interaction between dissimilar materials, usually organic compound interacting with inorganic ones. In order to improve this rate of injection and, by direct consequence the efficiency of this process, fundamental knowledge of this organic-inorganic interface must be gained. In this work the focus will reside solely on creating molecules capable of probing the interface between the indium tin oxide (ITO) and the donor layer. At this interface, the usual charge transfer being transferred is the hole. Chapters 2 and 3 detail the synthesis and photophysical characterization of porphyrin-perylene diimide (Por-PDI) and porphyrin-fullerene (Por-C₆₀) molecular dyads. The idea behind these moieties is that covalent attachment of these species to ITO should lead to a robust ohmic contact. Since these molecular dyads are capable of producing charge-separated states after photoexcitation, they should have the capacity to produce a radical-cation in close proximity to the ITO. This will translate to a capacity for probing the dynamics of the hole injection at this interface. Studies performed demonstrate that in fact these dyads are capable of producing a charge-separated state upon photo-excitation. The lifetimes of these states were determine to be 35 ps and 3 ns for the Por-PDI and Por-C₆₀ respectively. Chapter 4 takes a different turn. It is focused on the application and extension of a solvent-free synthesis of metallated phthalocyanines (Pcs). Shown in chapter 4 is the synthesis of a series of metallated Pcs using various transition metals and group 3 elements. Photophysical and electrochemical investigation of these materials shows that they have near-infrared absorption and relative high HOMO levels making them potential candidates for OPV applications. In addition, they displayed non-linear optical behavior due to their highly polarizable pi-systems and the presence of axial susbtituents. Finally Chapter 5 describes the synthesis and characterization of porphyrin possessing rigid linkers. This chapter also shows the further directions in which the various ideas presented in this work could be driven.

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8

Valenanzo, Loredana. "Calculation of fully non-adiabatic properties of the hydrogen molecular cation and its isotopomers." Thesis, University of Southampton, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274534.

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9

Scharf, Sebastian. "Identi cation of novel molecular factors involved in individual stress vulnerability." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-150881.

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10

Ilie, Alina. "Molecular characterization of the organellar-type alkali cation/proton exchanger NHE6." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=96826.

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Mammalian alkali cation/proton exchangers, more commonly known as sodium/proton exchangers (NHEs) are a family of transmembrane proteins that mediate an electroneutral exchange of Na+ (or K+) and protons across cellular membranes, thereby regulating intracellular pH and volume homeostasis. Eleven different isoforms have been identified, which differ in their tissue distribution, subcellular localization, and function. The organellar-type NHE6 isoform is widely distributed in tissues, but is enriched in brain, heart, and muscle. In order to elucidate the native distribution of NHE6 and to identify some of the mechanisms underlying its trafficking and function, a rabbit polyclonal antibody was generated. Utilizing this antibody in polarized human SH-SY5Y neuroblastoma cells, endogenous NHE6 was detected in transferrin receptor-containing vesicles in the soma and neurite processes. In mouse hippocampal organotypic slice cultures, NHE6 was detected within the soma, as well as dendritic shafts and spines of CA1 pyramidal cells. Ultrastructural analysis of mouse hippocampus and cortex revealed the presence of NHE6 positive signals predominantly in dendrites, occasionally adjacent to postsynaptic densities, and to a minor extent in some presynaptic terminals. N-glycosylation of proteins is involved in different aspects of protein function, such as folding, trafficking, stability and activity. To identify the glycosylation site(s) and their potential role in NHE6 function, mutagenesis analysis in combination with different biochemical assays and confocal microscopy were used. Our results revealed that asparagine 128 is the sole target for the N-glycosylation of the transporter. Furthermore, glycosylation was involved in promoting efficient export of the exchanger to the cell surface and for optimal transport activity within recycling endosomes.The NHEs have been shown to be regulated in part through the interaction of the cytosolic C-terminal domain with numerous interacting partners, depending on the isoform. In order to identify novel interacting proteins involved in the regulation of NHE6, a yeast two-hybrid screen of a human brain cDNA library was conducted using the C-tail of NHE6 as bait. Two of the clones identified encoded the receptor for activated protein kinase C 1 (RACK1), a scaffolding protein involved in numerous protein interactions and biological functions. Direct interaction of these two proteins was confirmed in vitro and in vivo. Depletion of RACK1 by siRNA resulted in increased total cellular expression and cell surface abundance of NHE6.Recently mutations in NHE6 have been linked to X-linked mental retardation, with a phenotype closely resembling that of Angelman syndrome. One of the mutations resulted in deletion of two residues (Glu255/Ser256) in the predicted transmembrane domain seven. To investigate the molecular mechanisms underlying the phenotype observed, we generated epitope-tagged variants of NHE6 bearing the deletion and showed that they display deficient processing and maturation, as well as markedly reduced stability in cells. Furthermore, the mutant protein is mislocalized in cells and targeted to an ill-defined acidic compartment. Preliminary results show that depletion of NHE6 in neurons resulted in decreased dendritic branching and disappearance of dendritic spines. We propose that the mutant protein is non-functional; thereby vesicular trafficking is impaired, resulting in deficient dendritic spine growth and maintenance.
Les échangeurs de Na+/H+ (NHEs) sont des protéines transmembranaires qui catalysent l'échange électroneutre de Na+ (ou K+) et de protons à travers les membranes cellulaires, régulant ainsi le pH intracellulaire et l'homéostasie du volume cellulaire. Jusqu'à présent, on été identifié onze isoformes, qui diffèrent dans leur distribution tissulaire, localisation subcellulaire, et leur fonction. L'isoforme NHE6 est largement distribué dans les tissus, mais il est plus exprimé dans le cerveau, le cœur et les muscles.Afin de déterminer la distribution native du NHE6 et d'identifier certains des mécanismes sous-jacents de son trafic et de sa fonction, on a crée un anticorps polyclonal. En utilisant celui-ci pour le marquage des cellules polarisées SH-SY5Y de neuroblastome, le NHE6 endogène a été détecté dans des vésicules contenant le récepteur de la transferrine, dans le corps cellulaire (soma) et au niveau des neurites. Dans des cultures cellulaires de l'hippocampe, le NHE6 a été détecté dans le soma et dans les dendrites ainsi que dans les épines des cellules pyramidales CA1 L'analyse ultrastructurale de l'hippocampe et du cortex de souris a révélé la présence des signaux positifs de NHE6 principalement dans les dendrites, parfois à côté de la région post-synaptique hyperdense, et dans une moindre mesure dans certaines terminaisons présynaptiques.La N-glycosylation des protéines est impliquée dans de différents aspects de la fonction des protéines, comme le pliage, le trafic, la stabilité et l'activité. Pour identifier les sites de glycosylation et leur rôle potentiel dans la fonction de NHE6, ont a utilisé la mutagenèse, en combinaison avec différents dosages biochimiques et la microscopie confocale. Nos résultats ont révélé que l'asparagine 128 est la seule cible de la N-glycosylation du transporteur. En outre, nous avons démontré que la glycosylation est nécessaire pour l'exportation efficace de l'échangeur à la surface cellulaire, ainsi que pour une l'activité optimal dans les endosomes de recyclage.Afin d'identifier des nouvelles protéines impliquées dans la régulation de NHE6, nous avons utilisé un système de double-hybride de levure. On a dentifiés deux clones qui codent le récepteur de la protéine kinase C (RACK1), une protéine d'échafaudage impliquée dans les interactions entre protéines. L'interaction directe de ces deux protéines a été confirmée in vitro et in vivo. L'utilisation de siRNA contre RACK1 conduit à une augmentation de l'expression cellulaire et de la densité sur la surface cellulaire du NHE6.Récemment, des mutations dans NHE6 ont été liées à un syndrome ressemblant à celui du syndrome d'Angelman. Une de ces mutations conduit a la suppression de deux résidus (Glu255/Ser256) dans le domaine sept transmembranaire. Pour étudier les mécanismes moléculaires sous-jacents au phénotype observé, nous avons généré des variantes de NHE6 portant la suppression, qui on montré une maturation inadéquate, ainsi qu'une stabilité réduite dans les cellules. En outre, la protéine mutante est mal-localisée dans les cellules et se trouve dans un compartiment acide mal défini. Des résultats préliminaires montrent que l'utilisation de siRNA contre NHE6 entraine une baisse de ramification dendritique, ainsi que la disparition d'épines dendritiques dans des neurones. Nous proposons que la protéine mutante n'est pas fonctionnelle, et que le trafic vésiculaire intracellulaire est altéré, ce qui peut entraîner une déficience dans le développement de dendrites.

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11

Scott, Sharon Elizabeth. "Computational Approaches to Studying Organic Cation Sorption to Organic Matter." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1594139918499603.

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12

Chen, Xiaofei Verfasser], Markus [Akademischer Betreuer] [Albrecht, and Iris Marga [Akademischer Betreuer] Oppel. "Helicate-based cation triggered molecular springs / Xiaofei Chen ; Markus Albrecht, Iris Marga Oppel." Aachen : Universitätsbibliothek der RWTH Aachen, 2019. http://d-nb.info/1195238177/34.

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13

Oppermann, Malte. "Resolving strong field dynamics in cation states of CO2 via optimised molecular alignment." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/18049.

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In this thesis, the role of the molecular structure in strong field induced processes in CO2 is resolved by the use of optimised impulsive molecular alignment. Two processes were investigated: recollision induced ionisation and the dissociation of the molecular ion CO2+. Both processes are driven by the initial tunneling ionisation of CO2. Through the use of molecular alignment, the orbital symmetries of the involved molecular ionic states were resolved, revealing the internal molecular dynamics in the form of ionisation and excitation pathways. A novel data analysis procedure was developed to extract the alignment distribution and rotational temperature of the impulsively aligned molecular ensemble. This facilitated the optimisation of molecular alignment in mixed gas samples and was demonstrated for N2, O2 and CO2 seeded in Ar. The recollision induced or nonsequential double ionisation (NSDI) of CO2 was then studied in the molecular frame. The process was fully characterised by measuring the shape of the recolliding electron wavepacket and the angularly resolved inelastic electron-ion recollision cross section. The results reveal the contribution from both the ionic ground and first excited state of CO2+ to the NSDI mechanism. This study was extended to the strong field induced dissociation of impulsively aligned CO2+. It was found that dissociation is driven by a parallel dipole transition from the second excited ionic state B to the predissociating state C, whilst recollision excitation was shown to not play a role. The strong field induced coupling of the ionic states B and C could thus be controlled by the laser polarisation. The results obtained in this thesis further the understanding of population dynamics of cation states in strong field processes. This is of special interest for extending molecular strong field physics to the study of electronic degrees of freedom and their coupling to the nuclear motion.

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14

Corma, Avelino, Jörg Kärger, and Cordula Krause. "PFG NMR measurement of molecular diffusion in cation-free zeolites of type LTA." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-196454.

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15

Corma, Avelino, Jörg Kärger, and Cordula Krause. "PFG NMR measurement of molecular diffusion in cation-free zeolites of type LTA." Diffusion fundamentals 2 (2005) 87, S. 1-2, 2005. https://ul.qucosa.de/id/qucosa%3A14423.

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16

Chen, Xiaofei [Verfasser], Markus [Akademischer Betreuer] Albrecht, and Iris Marga [Akademischer Betreuer] Oppel. "Helicate-based cation triggered molecular springs / Xiaofei Chen ; Markus Albrecht, Iris Marga Oppel." Aachen : Universitätsbibliothek der RWTH Aachen, 2019. http://d-nb.info/1195238177/34.

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17

Reece, Mark T. "Functional characterization of OCTRL2 : an organic cation transporter expressed in the renal proximal tubules." Thesis, McGill University, 1998. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=20973.

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Chromosome 11p15.5 harbors a gene or genes involved in Beckwith Wiedemann Syndrome (BWS) and that confer(s) susceptibility to Wilms' tumor, rhabdomyosarcoma, and hepatoblastoma. PowerBLAST of P1 artificial chromosome clones from this region identified two novel transcripts with open reading frames encoding putative proteins of 253 and 424 amino acids. The larger of the transcripts was shown by Northern blot to be predominantly expressed in the fetal and adult liver and kidney. This transcript shares homology with integral membrane organic cation transporters, such as the tetracycline resistance proteins and bacterial multidrug resistance proteins; and was therefore designated ORCTL2 (organic cation transporter-like 2). An expressed sequence polymorphism provided evidence that the ORCTL2 gene exhibits "leaky" imprinting in both human fetal kidney and human fetal liver. Given the expression pattern of ORCTL2, it is possible that this gene may have a role in the development of phenotypes associated with BWS, including Wilms' tumor (WT). SSCP analysis on 51 sporatic WT samples did not identify any mutations in ORCTL2 which would implicate it in disease. Investigation of the transport properties of ORCTL2 show that this protein can confer resistance to chloroquine and quinidine when overexpressed in bacteria. Immunohistochemistry performed with anti-ORCTL2 polyclonal antibodies on human renal sections indicate that ORCTL2 is localized on the apical membrane surface of the proximal tubules. These results suggest that ORCTL2 may play a role in the transport of chloroquine and quinidine related compounds within the kidney.

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18

Greenlee, Jordan Douglas. "Study of cation-dominated ionic-electronic materials and devices." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/53401.

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The memristor is a two-terminal semiconductor device that is able to mimic the conductance response of synapses and can be utilized in next-generation computing platforms that will compute similarly to the mammalian brain. The initial memristor implementation is operated by the digital formation and dissolution of a highly conductive filament. However, an analog memristor is necessary to mimic analog synapses in the mammalian brain. To understand the mechanisms of operation and impact of different device designs, analog memristors were fabricated, modeled, and characterized. To realize analog memristors, lithiated transition metal oxides were grown by molecular beam epitaxy, RF sputtering, and liquid phase electro-epitaxy. Analog memristors were modeled using a finite element model simulation and characterized with X-ray absorption spectroscopy, impedance spectroscopy, and other electrical methods. It was shown that lithium movement facilitates analog memristance and nanoscopic ionic-electronic memristors with ion-soluble electrodes can be key enabling devices for brain-inspired computing.

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19

Hardy, Sarah Catherine. "Molecular and functional investigation of a novel non-selective cation channel involved in oxidative stress." Thesis, University of Aberdeen, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340625.

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20

Spångberg, Daniel. "Cation Solvation in Water and Acetonitrile from Theoretical Calculations." Doctoral thesis, Uppsala University, Department of Materials Chemistry, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3598.

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Metal ions solvated in aqueous, non-aqueous, and mixtures of solvents occur in many chemical contexts, for example in electrochemical applications and solvent separation. Solvated ions appear in high concentration in the living organisms, where their presence or absence can fundamentally alter the functions of life. In many of these cases, understanding the selective solvation and the dynamics of the ions is essential for the understanding of the processes involved.

Computer simulation provides a molecular level of detail of the solvation process usually not available from experiments. The quality of the interaction models employed in the theoretical description is of particular importance, since even rather small changes in the interaction can lead to substantial and qualitative differences.

This thesis describes the development of a sequence of increasingly refined analytical ion-solvent potentials from ab initio calculations for the systems Li⁺(aq), Na⁺(aq), Mg²⁺(aq), Al³⁺(aq), Li⁺(MeCN), Na⁺(MeCN), Li⁺(aq, MeCN), and Na⁺(aq, MeCN). Molecular dynamics simulations using these potentials were subsequently performed, and some key-properties computed. The reliability of the computed thermodynamical, structural and dynamical properties was scrutinized.

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21

Hamm, Laura Mae. "Calcium carbonate biomineralization: A theoretical and experimental investigation of biomolecular controls on nucleation and growth." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/27670.

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Organisms have evolved a remarkable ability to mineralize complex skeletons and functional biomaterials. These structures are nucleated and grown in close associaiton with macromolecular assemblages of proteins and polysaccharides that are implicated in regulating all stagees of mineralization. Because of this intimate association of organic with inorgaic components, many studies have investigated the effects of particular organic species on mineral morphology, phase, and growth rate. However, the diversity and species-specific nature of the organic assemblages associated with biominerals across a wide variety of taxa, has limited our understanding of how organisms use biomolecules to regulate skeletal formation. It is clear that a mechanistic picture of biomolecular controls on mineralization requires molecular-level investigations of the interplay between organic and inorganic components at all stages of crystallizaiton. This dissertation presents the findings from theoretical and experimental studies of the physical mechanisms that underlie biomolecule controls on mineral formation. Molecular dynamics simulations probe the effects of acidic molecules on the hydration of alkaline earth cations. After first calculating baseline hydration properties for magnesium, calcium, strontium, and barium, I determine the effects of carboxylate-containing molecules on cation hydration state as well as the kinetics and thermodynamics of water exchange. Experimental work utilizes self-assembled monolayers as proxies for matrix macromolecules in order to understand their effects on CaCO3 nucleation kinetics and thermodynamics. Estimates of nucleation rates and barriers are made from optical microscopy data and correlated with measurements of crystal â substrate rupture force from dynamic force microscopy. These investigations show that an important function of biomolecules in directing mineralization lies in their ability to modulate cation hydration. Both chemical functionality and molecular conformation are influential in regulating the kinetics and thermodynamics of mineral nucleation, and these effects may be predicted by the strength of interaction between organic and inorganic components. These findings contribute to a mechanistic understanding of how organic matrices act to regulate biomineral formation. They demonstrate a plausible physical basis for how carboxyl-rich biomolecules accelerate the kinetics of biomineral growth and suggest roles for organic species in the nucleation and pre-nucleation stages of mineralization.
Ph. D.

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22

Cheng, Shijing. "Synthesis and Characterization of Cation-Containing and Hydrogen Bonding Supramolecular Polymers." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/77185.

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Non-covalent interactions including nucleobase hydrogen bonding and phosphonium/ammonium ionic aggregation were studied in block and random polymers synthesized using controlled radical polymerization techniques such as nitroxide mediated polymerization (NMP) and reversible addition-fragmentation chain transfer polymerization (RAFT). Non-covalent interactions were expected to increase the effective molecular weight of the polymeric precursors through intermolecular associations and to induce microphase separation. The influence of non-covalent association on the structure/property relationships of these materials were studied in terms of physical properties (tensile, DMA, rheology) as well as morphological studies (AFM, SAXS). Ionic interactions, which possess stronger interaction energies than hydrogen bonds (~150 kJ/mol) were studied in the context of phosphonium-containing acrylate triblock (ABA) copolymers and random copolymers. Phosphonium-containing ionic liquid monomers with different alkyl substituent lengths and counterions enabled an investigation of the effects of ionic aggregation of phosphonium cations on the polymer physical properties. The polymerization of styrenic phosphonium-containing ionic liquid monomers using a difunctional alkoxyamine initiator, DEPN2, afforded an ABA triblock copolymer with an n-butyl acrylate soft center block and symmetric phosphonium-containing external reinforcing blocks. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) of triblock copolymers revealed pronounced microphase separation at the nanoscale. Phosphonium aggregation governed block copolymer flow activation energies. In random copolymers, the phosphonium cations only weakly aggregated, which strongly depended on the length of alkyl substituents and the type of counterions. Acrylate random copolymers consisting of quaternary ammonium functionalities were synthesized using reversible addition-fragmentation chain transfer polymerization (RAFT). The obtained copolymers possessed controlled compositions and narrow molecular weight distributions with molecular weights ranging from Mn =50,000 to 170,000 g/mol. DMA evidenced the weak aggregation of ammonium cations in the solid state. Additionally, this ionomer was salt-responsive in NaCl aqueous solutions. Hydrogen bonding, a dynamic interaction with intermediate enthalpies (10-40 kJ/mol) was introduced through complementary heterocyclic DNA nucleobases such as adenine, thymine and uracil. Our investigations in this field have focused on the use of DNA nucleobase pair interactions to control polymer self-assembly and rheological behavior. Novel acrylic adenine- and thymine-containing monomers were synthesized from aza-Michael addition reaction. The long alkyl spacers between nucleobase and polymer backbone afforded structural flexibility in self-assembly process. Adenine-containing polyacrylates exhibited unique morphologies due to adenine-adenine π-π interactions. The complementary hydrogen bonding of adenine and thymine resulted in disruption of adenine-adenine π-π interactions, leading to lower plateau modulus and lower softening temperatures. Moreover, hydrogen bonding interactions enabled the compatibilization of complementary hydrogen bonding guest molecules such as uracil phosphonium chloride.
Ph. D.

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23

Bohinski, Timothy Blaise. "STRONG FIELD MOLECULAR IONIZATION: CONTROLLED DISSOCIATION IN RADICAL CATIONS WITH DYNAMIC RESONANCES AND ADIABATICALLY PREPARED LAUNCH STATES." Diss., Temple University Libraries, 2015. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/310686.

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Chemistry
Ph.D.
This dissertation investigates the electronic spectroscopy of a series of alkyl phenyl ketone radical cations and the dynamics of selective launch states in the strong field regime with tunable near infrared ultrashort laser pulses from 790 nm - 1550 nm coupled to mass spectrometric detection. Our method relies on tunable strong field laser pulses in the range from 1150 nm - 1550 nm to adiabatically ioinized gas phase molecules and prepare ions in the ground ionic state that serve as a launch state for future excitation and control. Adiabatic ionization is capable of transferring little energy to the molecule and producing a majority of a parent molecular ion in comparison to nonadiabatic ionization wherein multiple ionic states can be populated with an accompanying high degree of molecular fragmentation. We measure a dynamic resonance in the low lying electronic states of the acetopheone radical cation via preparation of a launch state with adiabatic ionization followed by a one photon transition within a single pulse duration which facilitates bond dissociation to produce the benzoyl ion. Experiments on acetophenone homologues and derivatives elucidate the structural dependence of the electronic resonance and supporting ab initio calculations identify the dynamic resonance along the molecular torsional coordinate between the ground ionic state, D0, and second excited state, D2. Post ionization excitation within the pulse duration transfers the ground state wavepacket to the D2 surface where the wavepacket encounters a three state conical intersection that facilitates the preferred bond dissociation. Time resolved photodissociation experiments measure the dynamics of the launch state, large amplitude oscillations and extended coherence times support the notion that adiabatic ionization populates a majority of the ground ionic surface. Control of the dissociation products is initiated from the launch state by varying the pump wavelength and probe intensity. Elimination of the D0 wavepacket with a 1370 nm reveals additional secondary dynamics that are attributed to wavepacket motion on the D2 surface. Finally, the effect of para substitution on the acetophenone radical cation is explored as a strategy to control the launch state wavepacket dynamics. Suppresion of the wavepacket dynamics are observed with the addition of alkoxy groups whereas extended coherence of the launch state dynamics approaching ~5 ps is observed upon trifluoromethyl substitution. A possible mechanism for the extended coherenece based on coupled torsional rotors is proposed.
Temple University--Theses

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24

Zhao, Qian. "Molecular dynamics simulation of interactions between clay minerals and a controlled organic phase." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47650.

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Engineered organoclays are 2:1 phyllosilicate soils that have been synthesized with a controlled interlayer organic phase to exhibit enhanced strength, lower compressibility, and stronger retention of organic compounds. Engineered organoclays are highly sorptive, and have a variety of potential engineering applications as sorbents or amendments in engineered earthen barrier systems. Previous studies examined the impact of the organic coating on a soil's physical properties; however, the geochemical behaviors of organoclays, especially their interaction with organic compounds at the micro-scale, remained relatively unquantified. This study investigated the engineering behavior of montmorillonite modified with a variety of quaternary ammonium cations (QAC clays) with controlled structure and density of loading. Molecular dynamics simulations were used to model the surfactant arrangement, geochemical processes in the QAC-clay interlayer, including organic compound sorption and mass transport, as well as the surface electrokinetics of suspended QAC-clay particles. All simulations were carried out based on the combined force field of ClayFF and the Consistent-Valence Force Field to ensure the accuracy of the simulation results, and results yielded insight into the prediction of synthesized QAC-clay behaviors as sorptive material for non-polar organic compounds.

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25

Jung, Silke. "Functional and molecular characterization of receptor activated cation currents in a vascular smooth muscle cell line: a role for TRPC channels." [S.l. : s.n.], 2002. http://www.diss.fu-berlin.de/2002/131/index.html.

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26

Dix, James. "Understanding the mechanism of permeation through graphene-based membranes using molecular dynamics simulations." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/understanding-the-mechanism-of-permeation-through-graphenebased-membranes-using-molecular-dynamics-simulations(68f5ea06-3ba5-4b2c-91e9-18b57bb2b6d7).html.

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The UN predicts that by 2050 there will water shortages throughout the globe. Current sources for safe, clean drinking water are being over mined and exhausted. Seawater provides an alternative water source, but a high salt content makes it unsuitable for the majority of applications. However, reverse osmosis lowers the salt content producing water that is safe for human consumption. Reverse osmosis uses a semi-permeable membrane to prevent the transport of salt but allows for the transport of water. Currently these membranes are susceptible to fouling and contamination, which reduces their efficiency. Graphene-oxide membranes offer a new material for reserves osmosis membranes. Sheets of graphene-oxide are stacked in a layered structure. The separation between the sheets can be controlled using physical confinement, resulting in limited ion permeation of abundant cations in seawater, like Na+ and K+. This is believed to be due to the separation of 0.76 nm between the graphene sheets, forcing the ions to lose its surrounding water molecules, making it unfavourable for the ion to travel through the membrane. Molecular dynamics simulations can give an atomic level insight into the molecular processes within GO membranes. Recent simulations have shown that charged species are attracted to graphene surfaces due to polarisation of the pi-electron system. This work has managed to incorporate these ion-pi interactions into molecular dynamics simulations. Including ion-pi interactions caused some ions, like Na+ and K+, to prefer to lose water molecules and reside at a graphene surface. This work observed the same phenomena when ions were confined to graphene channel ranging from 1.3 nm - 0.7 nm. This observation could have a large impact on whether dehydration is limiting the permeation of these two ions, or if there are additional processes that limit their molecular transport.

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Lebedel, Ludivine. "Exploiter des superacides pour générer et caractériser des espèces ioniques clés dans le domaine des glycosciences." Thesis, Poitiers, 2019. http://theses.univ-poitiers.fr/63048/2019-Lebedel-Ludivine-These.

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La réaction de glycosylation, qui permet de former la liaison glycosidique, joue un rôle clé dans l’accès aux glycanes et glycoconjugués biologiquement actifs qui sont de plus en plus complexes. Très utilisée en glycochimie, les détails du mécanisme de cette réaction font encore l’objet de nombreuses études, en particulier pour évaluer la formation d’une espèce clé, le cation glycosyle. La mise en évidence de ce type d’espèces ioniques est essentielle pour élucider le mécanisme de cette réaction. Néanmoins, l’existence de cet intermédiaire cationique en solution reste à confirmer du fait d’une durée de vie très courte en solution.A partir d’une méthode mise au point au laboratoire utilisant la chimie des sucres et la chimie des superacides combinées à la spectroscopie RMN in situ et à la modélisation moléculaire, ce travail de thèse a consisté à étudier des intermédiaires ioniques furtifs de la réaction de glycosylation. Tout d’abord, plusieurs donneurs de glycosyle possédant différentes substituants sur la position C-2 ont été étudiés en milieu HF/SbF5. Des dérivés 2-halogéno ont notamment permis de générer, stabiliser et observer les cations glycosyles correspondants grâce à une plus grande durée de vie dans le milieu HF/SbF5. Puis, cette méthode a été étendue à d’autres sucres et a mis en évidence différents intermédiaires réactionnels jusque-là théoriques qui ont été caractérisés. Enfin, une analogie a été établie entre les interactions multidentates existant entre le milieu superacide et un cation glycosyle non protégé formé in situ et l’état de transition de l’enzyme Béta-1,3-glucanase, permettant alors de proposer une similarité entre les cations glycosyles générés en milieu superacide et ceux formés dans un environnement enzymatique
The glycosylation reaction which forms glycosidic bond, contributes to access to biologically active and complex glycans and glycoconjugates. Used extensively in glycochemistry, the details of the mechanism of this reaction are the subject of many studies, in particular to evaluate the formation of the glycosyl cation. The observation and the characterization of these ionic species is essential to elucidate the mechanism of this reaction. The existence of this cationic intermediate in solution remains to be confirmed.Employing a method developed in the laboratory using glycochemistry and superacid chemistry combined with in situ NMR spectroscopy and molecular modelling, this project consists of studying furtive ionic intermediates of the glycosylation reaction. First, several glycosyl donors with different substituents at the position C-2 were studied in HF/SbF5. In particular, 2-halogeno derivatives were shown to generate the corresponding glycosyl cation and their stabilisation in superacid allowed their observation and deep analysis in HF/SbF5. Then, this method was extended to other sugars highlighting different reaction intermediates. Finally, the multidentate interactions of superacid medium with a naked glycosyl cation formed in situ were compared with the transition state of a Béta-1,3-glucanase allowing to evaluate any mimicry between these species generated in superacid and in enzymatic environment

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Mace, Amber. "Multiscale Modeling of Molecular Sieving in LTA-type Zeolites : From the Quantum Level to the Macroscopic." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-113024.

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LTA-type zeolites with narrow window apertures coinciding with the approximate size of small gaseous molecules such as CO2 and N2 are interesting candidates for adsorbents with swing adsorption technologies due to their molecular sieving capabilities and otherwise attractive properties. These sieving capabilities are dependent on the energy barriers of diffusion between the zeolite pores, which can be fine-tuned by altering the framework composition. An ab initio level of theory is necessary to accurately describe specific gas-zeolite interaction and diffusion properties, while it is desirable to predict the macroscopic scale diffusion for industrial applications. Hence, a multiscale modeling approach is necessary to describe the molecular sieving phenomena exhaustively. In this thesis, we use several different modeling methods on different length and time scales to describe the diffusion driven uptake and separation of CO2 and N2 in Zeolite NaKA. A combination of classical force field based modeling methods are used to show the importance of taking into account both thermodynamic, as well as, kinetic effects when modeling gas uptake in narrow pore zeolites where the gas diffusion is to some extent hindered. For a more detailed investigation of the gas molecules’ pore-to-pore dynamics in the material, we present a procedure to compute the free energy barriers of diffusion using spatially constrained ab initio Molecular Dynamics. With this procedure, we seek to identify diffusion rate determining local properties of the Zeolite NaKA pores, including the Na+-to-K+ exchange at different ion sites and the presence of additional CO2 molecules in the pores. This energy barrier information is then used as input for the Kinetic Monte Carlo method, allowing us to simulate and compare these and other effects on the diffusion driven uptake using a realistic powder particle model on macroscopic timescales.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

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Estébanez, Perpiñá Eva. "Crystal Structure of Human Granzyme B. Modelling of the Granzyme B-Cation-Independent Mannose-6-Phosphate Receptor Complex. Crystal Structure of Human Pro-Granzyme K. Crystal Structure of the Procarboxypeptidase from Helicoverpa armigera." Doctoral thesis, Universitat Autònoma de Barcelona, 2002. http://hdl.handle.net/10803/3477.

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Estructura Tridimensional de Granzima B humana
Granzima B es la proteina prototípica de la familia de serina proteasas que se encuentran en células NK y CTLs. GzmB induce apoptosis mediante activación de las caspasas, y está implicada en la etiología de la artritis reumatoidea. Hemos cristalizado y resuelto la estructura 3D de la GzmB humana a una resolución de 3.1Å. GzmB muestra un plegamiento similar al de catepsina G y quimasa humanas. GzmB exhibe una especificidad de substrato muy inusual ya que corta tras Asp, debido a la presencia de Arg226 en bolsillo de especificidad S1. El sitio de unión del substrato está diseñado para acomodar y cortar hexapéptidos, i.e. IETD_SG, secuencia presente en el lugar de activación de la caspasa-3 y de Bid, sus substratos fisiológicos. Esta estructura ayudará en el diseño de inhibidores que podrian ser usados en la cura de enfermedades inflamatorias crónicas.
Granzyme B y el Receptor Manosa-6-Fosfato Independiente de Cationes
GzmB cristalizó como dímero, mediante la interdigitación de las cadenas de azúcares unidas a Asn65 en los dos monómeros. GzmB es captada por las células mediante el Receptor Manosa-6-Fosfato Independiente de Cationes. Sugerimos que la GzmB dimérica sea la forma internalizada por las células diana. Hemos modelado cómo posiblemente GzmB se une a su receptor celular.
Estructura Tridimensional de pro-Granzyme K humana
Hemos determinado la estructura 3D de la pGzmK a una resolución de 2.2Å. pGzmK se parece más a una serina proteasa activa, a pesar de ser un zimógeno. Esta proteina carece de triada zimogénica y utiliza un nuevo mecanismo de estabilización de la forma inactiva.
Estructura Tridimensional de una Procarboxipeptidasa de Helicoverpa armigera. H. armigera es un insecto cuya plaga afecta a un gran número de países. Hemos determinado la estructura 3D de una nueva carboxipeptidasa (PCPAHa) de larvas de H. armigera, la primera resuelta de un insecto hasta la fecha. El zimógeno de PCPAHa muestra una estructura similar a las ya resueltas de mamífero. Su sitio de activación presenta el motivo (Ala)5Lys. Es curioso apreciar similar motivo ((Ala)6Lys) cerca del extremo N-terminal del enzima activo. Ser255 agranda el bolsillo S1´de especificidad y influencia las preferencias de substrato de ésta enzima. Hemos modelado el extremo C-terminal del LCI dentro del sitio activo de PCPAHa.
Crystal Structure of Human Granzyme B
Granzyme B is the prototypic member of the granzymes, trypsin-like serine proteinases localized in activated NK cells and CTLs. GzmB triggers apoptosis by activating the caspases, and is implicated in the etiology of rheumatoid arthritis. Human GzmB has been crystallized and its structure has been determined to 3.1 Å resolution. GzmB overall fold is similar to that found in cathepsin G and human chymase. GzmB exhibits an unusual substrate specificity as it cleaves after Asp residues due to the presence of Arg226 at the back of the S1-specificity pocket. GzmB substrate binding site is designed to fit and cleave hexapeptides, i.e. IETD_SG, sequence present in the activation site of caspase-3 and Bid, physiological substrates of GzmB. This structure would help in the design of inhibitors for a treatment of chronic inflammatory disorders.
Granzyme B and the Cation-Independent Mannose-6-Phosphate Receptor
Our crystal structure of GzmB unexpectedly revealed a dimer, mediated by the interdigitation of the sugar chains attached to Asn65 in the two monomers. The uptake of GzmB is effected by the cation-independent mannose-6-phosphate (M6P) receptor. We suggest that the GzmB dimer would be the form preferentially recognized by its receptor. To investigate the probable binding mode of GzmB to its cell receptor we have modeled the binding of the GzmB dimer to the M6P-receptor.
Crystal Structure of Human Pro-Granzyme K
We have determined the crystal structure of human pGzmK at 2.2 resolution. The overall fold of pGzmK is most similar to that found in active serine proteinases rather than in zymogens. An unusual feature of pGzmK is that the residues Ser32, His40 and Asp194 do not form a zymogen triad, while pGzmK uses a novel mechanism for zymogen stabilization.
Crystal Structure of a Procarboxypeptidase from Helicoverpa armigera
H. armigera is one of the most serious insect pests worldwide. We present the 2.5 Å crystal structure from this novel procarboxypeptidase (PCPAHa) from H. armigera larvae, the first one reported for an insect. PCPAHa zymogen has a 3D structure similar to the corresponding mammalian digestive carboxypeptidases. The activation site contains the motif (Ala)5Lys. It is noteworthy the occurrence of the same (Ala)6Lys near the C-terminus of the active enzyme. Ser255 enlarges the S1' specificity pocket and influences the substrate preferences of the enzyme. The C-terminal tail of LCI was modeled into PCPAHa active site.

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30

Mader, Dorathea Felicitas. "Relation structure - propriétés de commutation dans les matériaux à transition de spin : effet de nanostructuration et de dilution du cation métallique." Thesis, Nancy 1, 2011. http://www.theses.fr/2011NAN10124/document.

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Ces dernières années, de nombreux travaux de recherche ont été dédiés aux matériaux moléculaires à transition de spin à base de FeII, aussi bien du point de vue de la compréhension des phénomènes fondamentaux que de la mise en forme en vue d'applications. Ces matériaux présentent deux configurations électroniques inter-commutables sous l'effet d'une perturbation extérieure (bistabilité thermique et optique). Des interactions intra- et intermoléculaires fortes au sein du réseau cristallin peuvent conférer au matériau un comportement coopératif associé à des transitions de spin abruptes et un caractère hystérétique à l'origine d'un effet mémoire. La compréhension de l'origine de la coopérativité ainsi que sa maîtrise présentent à ce jour un intérêt certain. L'effet de la dilution métallique sur les propriétés de commutation photoinduites dans les composés FexZn1-x(btr)2(NCS)2.H2O est étudié par diffraction des rayons X sur monocristal. Un modèle microscopique expliquant les différents processus mis en jeu au cours de la transition (nucléation et séparation de phase) est proposé à partir d'une analyse structurale des données. Les effets de nanostructuration sont étudiés sur le polymère de coordination unidimensionnel [Fe(Htrz)2trz](BF4). Différents milieux inverses à base de tensioactif et d'organisation structurale variée (systèmes moléculaires organisés) ont été choisis pour une synthèse en environnement confiné (milieu micellaire inverse, phase cristal liquide hexagonale inverse (HII) et lamellaire (Lalpha)). Un lien entre la taille et la morphologie des particules, leur microstructure et leurs propriétés physico-chimiques est établi. Un intérêt particulier est porté à la dynamique de la réaction en milieu cristal liquide
In the last years, intensive research activity has been dedicated to iron(II)-based spin transition compounds, for a better understanding of the fundamental phenomena as within the scope of practical application. These molecular materials possess two electronic configurations, which are interchangeable by the application of an external perturbation (thermal and optic bistability). Strong electron-lattice coupling may lead to cooperative behaviour, consequently abrupt spin transitions and hysteretic behaviour at the origin of a memory effect. Understanding and controlling this property is of primary interest in fundamental and applied research. The influence of metal dilution on the photo-induced transitions in FexZn1-x(btr)2(NCS)2.H2O is investigated by X-Ray diffraction on single crystals. We suggest a microscopic model interpreting the dynamics of the phase transition (nucleation and growth mechanisms of spin-like domains) through a structural analysis of the diffraction data. The effects of nanostructuration on the physicochemical properties have been studied on the one-dimensional coordination polymer [Fe(Htrz)2trz](BF4). Different surfactant-based organized molecular systems with various structural organizations are chosen for the synthesis in confined environments: reverse micellar solutions as well as lamellar (Lalpha) and reverse hexagonal (HII) liquid crystal phases. A relationship between size and shape, microstructure and physicochemical properties is established with a specific attention to reaction dynamics in the liquid crystal phase

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Wurtz, Jean-Marie. "Logiciels infographiques de modelisation moleculaire : application a l'etude statique et dynamique d'un recepteur macrocyclique." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13147.

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Realisation de deux logiciels infographiques de modelisation moleculaire : 2d3d et mdnm, ecrits pour le systeme ps300 couple a un ordinateur vax. Avec 2d3d, construction de structures tridimensionnelles (3d) a partir du dessin interactif 2d, incorporant des contraintes structurales, afin de representer des structures 3d avec ou sans leur surface moleculaire. Emploi de mdnm pour representer les structures dynamiques issues de simulations par la methode de la dynamique moleculaire ou par la methode de monte carlo afin de visualiser de facon statique (par des vecteurs) ou dynamique des modes normaux de vibrations. Application a l'etude d'un recepteur macrotricyclique de synthese, le cryptand sc24 (neutre ou protone) et de divers cryptates de cations et d'anions en combinant 2d3d et mdnm pour des optimisations de mecanique moleculaires, des calculs de modes normaux de vibration, des simulations de dynamique moleculaire

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Tait, Claudia E. "Electron paramagnetic resonance studies of artificial supramolecular structures and biological systems." Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:b0535d55-89aa-4d89-b210-b49caf6b857e.

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The research described in this thesis employs a variety of Electron Paramagnetic Resonance (EPR) techniques for the study of the electronic and structural properties of artificial supramolecular porphyrin systems and of protein complexes of biological relevance. The electron delocalisation in the cationic radical and photoexcited triplet states of linear and cyclic Π-conjugated multiporphyrin arrays was investigated. In the radical cations, information on the extent of delocalisation can be inferred from the measurement of hyperfine couplings, either indirectly from the continuous wave EPR spectrum or directly using pulsed hyperfine EPR techniques. The results of room temperature EPR experiments showed complete delocalisation of the electron on the timescale of the EPR experiments, but frozen solution EPR measurements revealed localisation onto mainly two to three porphyrin units in the larger porphyrin systems. Information on the delocalisation of the triplet state in the same porphyrin systems is contained both in the hyperfine couplings and in the zero-field splitting (ZFS) interaction. The results outlined in this thesis show that the hyperfine couplings provide a much more accurate estimate of the extent of delocalisation. The trends in proton and nitrogen hyperfine couplings with the size of the porphyrin systems indicate uneven spin density distributions over the linear arrays, but complete delocalisation in the cyclic systems. Time-resolved EPR and magnetophotoselection experiments have shown a reorientation of the zero-field splitting tensor between a single porphyrin unit and longer linear arrays, resulting in alignment of the main optical transition moment and the Z axis of the ZFS tensor. Continuous wave and pulsed dipolar EPR techniques were employed for the determination of the structure of two different protein complexes, the homomultimeric twin-arginine translocase A (TatA) protein channel and the ferredoxin-P450 complex of the electron transport chain in Novosphingobium aromaticivorans. The interaction between nitroxide spin labels introduced at different positions of the TatA monomer was investigated in the complex reconstituted in detergent micelles by analysing the dipolar broadening of the EPR spectra and the results of three- and four-pulse Double Electron-Electron Resonance (DEER) measurements. In combination with results from NMR and molecular dynamics calculations, a structure for the channel complex was proposed. The structure of the ferredoxin-cytochrome P450 complex was investigated by orientation-selective DEER between nitroxide labels introduced on the cytochrome P450 protein and the iron-sulfur cluster of the ferredoxin. The distance and orientation information contained in the experimental DEER data was interpreted in terms of a structural model of the protein complex by orientation-selective DEER simulations combined with a modelling approach based on protein-protein docking.

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33

Fletcher, James. "Studies of atomic and molecular cations." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1420899/.

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Atomic and molecular cations have the potential to strongly influence a number of industrial, atmospheric and interstellar environments in which they are expected to be present. As a result, information on the generation and reactivity of positively charged species is invaluable when attempting to model and understand the physical and chemical processes taking place in such surroundings. This thesis reports a number of experimental investigations of the formation and reactivity of atomic and molecular cations. Firstly, a detailed study of the electron ionisation of sulphur dioxide (SO2) is presented. Relative precursor-specific partial ionisation cross sections for the fragment ions formed following electron ionisation of sulphur dioxide have been measured using time-of-flight mass spectrometry coupled with ion coincidence detection. These data quantify, for the first time, the formation of all fragment ions, relative to the formation of SO2+, via single, double and triple electron ionization of SO2. Secondly, the investigations of the bimolecular reactivity of a number of doubly (I2+ and N22+) and triply charged (I3+, Xe3+, CS23+) reactants are presented. A crossed-beam mass spectrometer was used to identify ion-molecule reaction products. The doubly and triply charged (I2+ and I3+/Xe3+) reactants are shown to participate in processes involving substantial rearrangement of chemical bonds. This reactivity can be encapsulated using a simple electrostatic model and energetic arguments. Furthermore, the same model has been updated to account for the results observed following the reactions of atomic trications. A different mass spectrometer, equipped with a position-sensitive coincidence ion detector, was then used to explore the dynamics of reactions involving first a molecular dication (N22+) with various low-mass organic molecules and then atomic (Xe3+) and molecular trications (CS23+). Product ion velocities determined using this technique can be used to explore the reaction energetics and angular scattering distributions for individual ion-molecule reaction channels. In turn, the interpretation of these data allow the identification of reaction mechanisms. The range of reactions exhibited in all of these studies is surprisingly diverse, clearly indicating a complex chemistry for collision systems involving dicationic and tricationic reactants.

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Etchebest, Catherine. "Etudes theoriques d'un canal ionique transmembranaire : la gramicidine a." Paris 6, 1987. http://www.theses.fr/1987PA066049.

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35

Webb, Alexander. "Imaging the photodissociation dynamics of molecular hydride cations." Thesis, University of Bristol, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.492462.

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The work presented in this thesis constitutes an imaging study of the photodissociation of state-selected molecular cations, each of which was prepared by (2+1) resonance-enhanced multiphoton ionisation (REMPI).

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36

Chatelain, Lucile. "Conception d'assemblages polymétalliques d'uranium pour le développement de molécules aimants." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAV076/document.

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L’étude de la chimie des actinides est essentielle dans le cadre de la technologie nucléaire pour le développement de nouveaux combustibles, pour l’étude du retraitement des déchets nucléaires et la migration des actinides dans l’environnement mais aussi pour la compréhension fondamentale des interactions actinide/ligand et la formation de liaisons multiples. Les propriétés magnétiques des molécules polymétalliques d’actinides sont particulièrement intéressantes pour explorer la communication magnétique entre différents centres métalliques. De plus, ces molécules ont été identifiées comme particulièrement prometteuses pour la conception de molécules aimants. L’uranium a une grande réactivité redox notamment due à ses multiples degrés d’oxydation accessibles et forme aisément des assemblages polynucléaires. Néanmoins, très peu de synthèses contrôlées de complexes polymétalliques d’uranium et de neptunium ont été décrites dans la littérature. La première approche de ce travail repose sur la synthèse de clusters oxo/hydroxo d’uranium à partir de l’hydrolyse contrôlée d’uranium tétravalent en présence d’un ligand organique rencontré dans l’environnement. Cette étude a mené à une famille de clusters aux topologies originales, dont la taille varie en fonction des conditions réactionnelles employées. Cependant les clusters obtenus ne mènjavascript:nouvelleZone('abstract');_ajtAbstract('abstract');ent pas à des propriétés de molécules aimants. Dans le but de favoriser une plus grande interaction entre les métaux par le ligand pontant, l’interaction cation-cation a été utilisée pour la synthèse rationnelle d’assemblages d’uranyle(V). Par le passé, peu de complexes d’uranyle(V) ont été isolés à cause de son instabilité vis-à-vis de la dismutation ; cependant, l’optimisation du ligand organique et des conditions de synthèse ont finalement permis de stabiliser l’uranyle(V). Nous avons utilisé des complexes stables d’uranyle(V) comme brique de base pour former des molécules hétéronucléaires avec des métaux 3d et 4f. Un réglage fin des conditions de réactions a mené à une conception rationnelle d’assemblages discrets ou polymériques. L’étude des propriétés magnétiques de ces assemblages d’uranium a mis en valeur des propriétés de molécules ou chaînes aimants avec de hautes valeurs d’énergie de relaxation. L’uranyle(V) a également été utilisé comme modèle structural du neptunium qui est plus radioactif permettant d’isoler un complexe isostructural homométallique de neptunyle(V) grâce à des conditions réactionnelles similaires. Finalement, des ligands nitrures favorisant la formation de liaison multiples uranium-ligand, ont été utilisés pour construire de nouveaux complexes binucléaires d’ujavascript:nouvelleZone('abstract');_ajtAbstract('abstract');ranium supportés par des ligands silanols. De nouvelles molécules, sans précédent, contenant des nitrures comme ligand pontant associés à de l’uranium au degré d’oxydation +III ont été isolées et caractérisées
The study of actinide chemistry is not only essential for the development of nuclear fuel, nuclear fuel reprocessing or environmental clean up, but also for the understanding of fundamental actinide/ligand interactions and multiple bounding. The magnetic properties of polynuclear actinide molecules are of significant interest to investigate the magnetic communication between the metallic centres. Furthermore, they are highly promising for the design of molecular magnets. Uranium undergoes redox reactions due to a wide range of available oxidation states and easily forms polynuclear assemblies. However, only a few controlled synthetic routes towards these polynuclear uranium assemblies are described in the literature. In this context, the first part of this work was dedicated to the synthesis of oxo/hydroxo uranium clusters from the controlled hydrolysis of tetravalent uranium in the presence of an environmentally relevant ligand. This led to the synthesis of clusters with novel topologies, for which size could be varied as a function of the reaction conditions employed. However, the obtained clusters do not behave as SMM. In order to gain a stronger interaction between metallic centres, the cation-cation interaction was used to rationally design polynuclear uranyl(V) complexes. The isolation of uranyl(V) complexes had been limited in the past by its disproportionation, however, a fine tuning of the organic ligand and reaction conditions finally allowed to stabilise uranyl(V). We used stable uranyl(V) units as building block to form heteronuclear complexes with 3d and 4f metals with polymeric or discrete structures. The study of the magnetic properties of the uranium polynuclear assemblies was carried out and revealed single molecule or chain magnet behaviours with high energy barriers. The uranyl(V) unit was also used as a structural model for the more radioactive neptunium element, allowing the isolation of an isostructural trinuclear neptunyl(V) assembly in similar reaction conditions. Finally, the use of a nitride ligand as a bridging unit, allowing the formation of uranium-ligand multiple bonds, was explored to build novel di-uranium complexes supported by siloxy ligands. Nitride molecules containing unprecedented uranium in the +III oxidation state were isolated and characterised

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37

Bulat, Muhammer. "Molecular cluster cations of carbon monoxide and carbon dioxide." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2010. http://dx.doi.org/10.18452/16246.

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Diese Dissertation handelt vom metastabilen Zerfall und von der Oberflächenwechselwirkung im hyperthermalen Energiebereich relativ schwach gebundener molekularer Kohlenmonoxid und Kohlendioxid Clusterkationen mit einer Edelstahloberfläche und einer Siliziumoberfläche. Im Rahmen dieser Arbeit wurde ein hierfür geeignetes spezielles Flugzeitmassenspektrometer entwickelt und aufgebaut. Entwurf, numerische Optimierung der Auflösung, ionenoptische Simulationen und Aufbau der jeweiligen Komponenten wie Elektronenquellen, Beschleuniger, Ablenkplatten, Massenfilter und Reflektron werden detailliert beschrieben. Das entwickelte Flugzeitmassenspektrometer besitzt mit einer kompakten Gesamtfluglänge von ~1.5m eine hohe Massenauflösung von m/Delta m = 3000. Es bietet die Möglichkeit, eine Massentrennung von Clusterionen mit einer Größe von bis zu n = 190 vorzunehmen. Diese massenselektierten Clusterionen können daraufhin auf metastabilen Zerfall und auf ihre Wechselwirkung mit einer Oberfläche untersucht werden. Dazu wurden Kohlendioxid-Clusterionen mit n
This thesis deals with the metastable decay and the surface scattering in the hyperthermal energy range of relatively weakly bound molecular cluster cations. With carbon monoxide and carbon dioxide two related model systems were chosen for a systematic size dependent study. Surface impact experiments were carried out with stainless steel and silicon surfaces. Results were obtained by a new, reflectron time-of-flight mass spectrometer (Re-TOFMS). Additional to the experimental data we present in this work a detailed description of the instrumental design considerations, numerical optimization, ion optical simulations. Hence each ion optical component like electron guns, accelerator, deflector, mass gate and reflectron are described. Despite the compact dimensions with a total flight length of ~1.5m the developed instrument possesses a high mass resolution above m/Delta m = 3000. Additionally it offers the possibility to perform mass separation of big cluster ions with sizes n

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38

Vieuxmaire, Olivier P. J. "Photodissociation dynamics of interhalogen molecules and cations." Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.427909.

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39

Jafou, Olga. "Complexation of macrocycles with lanthanide cations : a physicochemical study." Thesis, University of Surrey, 1999. http://epubs.surrey.ac.uk/844344/.

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This thesis investigates the complexing properties of synthetic macrocyclic ligands such as calix[4]arenes (L1-L6) and cryptand 222 (L7) towards lanthanide(III) cations in dipolar aprotic media (acetonitrile and N,N-dimethylformamide) at 298.15 K. Molecular modelling studies performed on calix[4]arene derivatives suggested that solvent molecules such as acetonitrile and N,N-dimethylformamide interact with the hydrophobic cavity, thus inducing conformational changes on these ligands, 'preorganising' them for complexation. 1H NMR complexation experiments established the presence of interactions between the hydrophilic cavity of calix[4]arene derivatives and the metal cations and revealed the sites of complexation of the ligands. Conductance measurements clearly demonstrated that 1:1 and 2:1 metal cation : ligand stoichiometries are found with these cations in acetonitrile. The thermodynamics of complexation of macrocyclic ligands and lanthanide(III) cations in acetonitrile and in N,N-dimethylformamide at 298.15 K was derived from titration microcalorimetry. Stability constants were also determined by the competitive potentiometric method using silver electrodes. Excellent agreement was found between the data derived from calorimetry and those derived by potentiometry. The complexation process between these cations and these ligands was enthalpically controlled for all systems studied. Enthalpy-entropy compensation effects were observed in the complexation of 5,11,17,23-tetrakis-(1,1-dimethylethyl)-25,27-bis[2-(methylthio)ethoxy]-26,28-bis[2(diethylamine)ethoxy]calix[4]arene, L1 and the different lanthanide(III) cations in acetonitrile, as well as L1, L7 and [tetrakis(N,N-diethylaminoethyl)oxyl]p-tert-butylcalix[4]arene, L2, in N,N-dimethyl formamide, as suggested by the absence of significant variations in the free energies of complexation in each case. As far as p-tert-butylcalix[4]arene tetradiisopropyl acetamide, L3, is concerned, a selective behaviour was observed for these cations in acetonitrile with the highest stabilities found for gadolinium and europium. Metal-ion complexes were isolated based on their stability and the solution thermodynamics of the free and complexed salts was investigated. Lastly, the complexation process in the two solvents was discussed, taking into account the differences in solvation of the reactants and the product in these solvents.

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40

Plettenberg-Halac, Sandra [Verfasser], Frank [Akademischer Betreuer] Wehner, and Philippe [Gutachter] Bastiaens. "Zelluläre Volumenregulation als Qualitätsparameter der Kryokonservierung sowie zur Identifizierung der molekularen Bestandteile des hyperton aktivierten Kationen Kanals : Cell volume regulation as a quality parameter for cryopreservation for the identification of the molecular correlates of hypertonicity induced cation channels / Sandra Plettenberg-Halac. Betreuer: Frank Wehner. Gutachter: Philippe Bastiaens." Dortmund : Universitätsbibliothek Dortmund, 2012. http://d-nb.info/1104735970/34.

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41

Boffelli, Jeoffrey. "Cοllisiοns réactives entre électrοns et catiοns d'hydrures : apprοches théοriques et applicatiοns dans les milieux iοnisés hοrs-équilibre". Electronic Thesis or Diss., Normandie, 2024. http://www.theses.fr/2024NORMLH19.

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Les collisions de molécules par impact d'électrons sont présentes dans les milieux ionisés froids tel que les nuages interstellaire, les atmosphères de planètes et les plasma froids. Avec assez d'énergie pour se déplacer et s'extraire, les électrons collisionnent et réagissent avec d'autres espèces dans leur environnement formant des précurseurs de molécules plus complexes ainsi que détruisant d’autres espèces, permettant la redistribution d’énergie et de matière. Les chercheurs expérimentaux et théoriques travaillent main dans la main pour améliorer en continue leur capacité de mesure et de description de la cinétique de ces milieux. Des appareils de mesures tel que les anneaux de stockage (e.g. CSR) sont maintenant capables de produire des mesures avec une résolution d’état à état. D’autre part, les études théoriques, elles, ne sont pas restreintes par des limitations physiques (e.g. finance) ou chimiques (e.g. toxicité) mais restent, comme les expériences, longues à mener.Ce travail de thèse porte sur deux approches théoriques et leurs applications pour étudier différents processus de trois cations moléculaires diatomiques. Premièrement, nous étendons l’étude précédente de notre groupe sur la recombinaison dissociative de CF+ en prenant en compte plus d’états dissociatives (venant de la symétrie neutre 4Π), en produisant des rapports de branchements et en calculant des sections efficaces et des vitesses de réactions pour l’excitation vibrationnelle (en utilisant l’approche SW-MQDT). Malgré que la structure rotationnelle soit négligée, et qui devrait être étudié dans un travail future, on observe un bon accord avec les résultats expérimentaux des anneaux de stockage pour les rendements venant du processus de recombinaison dissociative. Deuxièmement, nous étendons à haute énergie, l’étude de BeH+ précédente de notre groupe à basse énergie en incluant le processus d’excitation dissociative à travers la discrétisation des continuum d’ionisation et en prenant en compte des états dissociatives plus haut énergétiquement, permettant la production de sections efficaces et de vitesses de réactions pour la recombinaison dissociative, l’excitation dissociative et les transitions vibrationnelles (en utilisant l’approche SW-MQDT). En fin, nous étudions la recombinaison dissociative de CF+ en utilisant une approche différente appelée RMT-MQDT, où les couplages électroniques et les états dissociatives n’ont pas besoin d’être calculés de manière explicite, basée sur la théorie de la R-matrice pour calculer la matrice de diffusion à géométrie fixée électronique et aussi basée sur la théorie de la MQDT --- pour traiter le mouvement nucléaire (changement de repère) et prenant en compte les séries d’états de Rydberg (défaut quantiques avec CCEP). Un bon accord est trouvé avec l’expérience des anneaux de stockage lorsque la structure rotationnelle de la molécule est pris en compte
Electron-impact collisions of molecules are present in cold ionized media such as interstellar clouds, planetary atmospheres and cold plasma. With enough energy to move about and escape from capture, electrons collide and react with other species in their environment forming precursors of more complex molecules and destroying species, allowing for redistribution of energy and material. Experimental and theoretical researchers are working hand-in-hand to continuously improve their respective ability to probe and to describe the kinetic of such media. Experimental devices such as storage-rings (e.g. CSR) are now able to produce measurements with state-to-state resolution. On the other hand, theoretical studies are not restricted by physical (e.g. finance) or chemical (e.g. toxicity) limitations while still being time-consuming. This work is about two theoretical approaches and their applications to investigate different processes for three diatomic molecular cations. Firstly, we extend our group previous dissociative recombination study of SH+ by accounting for more dissociative states (coming from the 4Π neutral symmetry), by producing branching ratios and by calculating vibrational excitation cross sections and rate coefficients (using the SW-MQDT approach). While the rotational structure of the molecule is neglected and should be investigated in a future work, good agreement is found with the storage-ring measurements for the yields from the dissociative recombination process. Secondly, we also extend our group previous low energy study BeH+ to high energy including the dissociative excitation process through discretized ionization continua and by accounting for higher-lying dissociative states, allowing the production of cross sections and rate coefficients for the dissociative recombination, dissociative excitation and vibrational transitions (using the SW-MQDT approach). Finally, we investigate the dissociative recombination of CF+ using a different approach called RMT-MQDT, where electronic couplings and neutral dissociative states do not need to be explicitly calculated, based on R-matrix theory to calculate the electronic fixed-geometry scattering matrix and based also on MQDT theory --- for the treatment of the nuclear motion (frame transformation) and accounting for the Rydberg series of states (quantum defect with CCEP). Good agreement is found with the storage-ring experiment when accounting for the rotational structure of the molecule

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42

Lin, Song. "Elucidation of the Cation−π Interaction in Small-Molecule Asymmetric Catalysis." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11132.

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The cation–π interaction has been long-established to play an important role in molecular recognition, supramolecular chemistry, and molecular biology. In contrast, its potential application in small-molecule catalysis, especially as a selectivity-determining factor in asymmetric synthesis has been overlooked until very recently. This dissertation begins with an extensive literature review on the state-of-the-art research on the application of cation–π interactions in non-enzymatic catalysis of organic and organometallic transformations. The research in this field has been largely inspired and guided by the related biosynthetic systems incorporating the same type of interactions.

Chemistry and Chemical Biology

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Dolman, Mark. "Synthetic host molecules for cations and alkyl ammonium salts." Thesis, University of Liverpool, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385149.

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Ji, Ming Chao. "Molecular relaxation dynamics of Anthracene cations studied in an electrostatic storage ring." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10051.

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Les molécules hydrocarbures aromatiques polycycliques (HAP) sont à l'heure actuelle considérées comme probablement responsables des bandes d'émission infrarouge non identifiées du milieu interstellaire (MIS). La dynamique de refroidissement des molécules HAP est essentielle pour estimer leur photo-stabilité, leur durée de vie et les distributions de taille dans le MIS. Au cours des dernières années, les expériences s'appuyant sur le stockage électrostatique d'ions moléculaires ou d'agrégats sont devenus des outils puissants pour étudier leur refroidissement dans une large gamme de temps allant de la microseconde à quelques secondes. En général, l'étude des courbes de déclin associées aux processus de dissociation dans le cas des cations ou bien de détachement d'électrons dans le cas des anions fournit des informations sur l'évolution de l'énergie interne des ions stockés. Dans ce travail de thèse, le refroidissement de cations d'anthracène a été étudié dans un anneau de stockage électrostatique compact, le Mini-Ring, jusqu'à 8 ms. Les courbes de déclin spontané provenant de la dissociation par émission de fragment C2H2 ou H neutres montrent trois régions distinctives. Ces trois régions indiquent différents régimes de refroidissement en fonction du temps de stockage, la dissociation domine pour les temps inférieurs à 1 ms, l'effet de l'émission radiative entre alors en compétition avec la dissociation puis domine au-delà de 3 ms
The polycyclic aromatic hydrocarbon (PAH) molecules have been considered as possible carrier of the unidentified infrared emission bands from the interstellar medium (ISM) for about thirty years. The cooling dynamics of the PAH molecules which is essential to estimate their photostability and therefore their lifetime and size distributions in the ISM, has attracted numerous theoretical and experimental studies. In recent years, electrostatic storage devices (ESD) became powerful tool to investigate the cooling regime of molecules and clusters in a large time range from microseconds to seconds. Generally speaking, the decay of the emitted neutral yields due to dissociation of molecular cations or electron detachment of anions in such experiments carries information on the internal energy of the stored molecular ions. In this thesis work, the cooling regimes of anthracene cations are studied by following the time evolution of the internal energy distribution (IED) of the stored anthracene cations. A spontaneous neutral yield curve obtained from the stored molecular ions as a function of the storage time shows three distinguishable regions. The three regions indicate different cooling regimes at corresponding storage time range, i.e., the dissociation mechanism of the molecule dominates at storage time t < 1 ms, quenching of the dissociation by radiative cooling processes occurs during 1 < t < 3 ms and radiative cooling governs at t > 3 ms

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Souza, James Alves de. "Simulações por dinâmica molecular de compostos do tipo ABO3 (SrTiO3 e CaTiO3)." Universidade Federal de São Carlos, 2009. https://repositorio.ufscar.br/handle/ufscar/5016.

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Made available in DSpace on 2016-06-02T20:16:45Z (GMT). No. of bitstreams: 1 2261.pdf: 6647837 bytes, checksum: 5f3d49f4f65a3ec465ca7904f635b5f9 (MD5) Previous issue date: 2009-02-26
Universidade Federal de Minas Gerais
Using the classical molecular dynamics simulations, Perovskites systems composed by oxides (ABO3), in particular SrTiO3 and CaTiO3, were performed. The titanates are easily prepared as polycrystalline ceramics; chemically and mechanically stable they can be characterized in various temperature and pressure conditions. These provide us reliable experimental results for construction and consolidation of theoretical models. Another important fact is that these materials have wide variety of technological applications and many important properties as well as the phase transitions arising from the effect of temperature and pressure. That can be explored to understand the interactions among its constituents. The effective interatomic potential used has the same functional form of the potential proposed by Vashishta and Rahman and it s composed by the sum of terms Coulomb interaction, van der Waals, esthereometric and dipole-induced. The system was treated in (N, V, E) and (N, P, H) ensembles to verify the influence of temperature and pressure application on structural and dynamics properties of perovskites. The method used allowed us to describe various properties such as thermal expansion coefficient, angles distribution, coordination number, elastic properties, pair distribution function, density of vibrational states, Debye-Waller factor and so on. The phase transitions of systems were explored showing fantastic results.
Utilizando o método da Dinâmica Molecular clássica foram realizadas simulações de sistemas perovskitas formados por óxidos (ABO3), em particular SrTiO3 e CaTiO3. A vantagem em trabalhar com estes materiais é que os titanatos são facilmente preparados como cerâmicas policristalinas, são química e mecanicamente muito estáveis, o que torna possível caracterizálos em várias condições de temperatura e pressão, nos proporcionando resultados experimentais confiáveis para construção e consolidação de modelos teóricos. Outro fato importante é que estes materiais possuem ampla aplicabilidade tecnológica além de propriedades como transições de fase decorrentes do efeito de temperatura e pressão que podem ser exploradas para o melhor entendimento das interações entre seus constituintes. O potencial interatômico efetivo utilizado possui a mesma forma funcional dos potenciais propostos por Vashishta e Rahmann sendo composto pela soma dos termos de interação de Coulomb, de van der Waals, estereométrica e carga-dipolo induzido. Os sistemas foram tratados nos ensembles microcanônico (N,V,E) e isobárico-isoentálpico (N,P,H) para verificação da influência da temperatura e aplicação de pressão em suas propriedades estruturais e dinâmicas. O método empregado nos permitiu descrever de maneira satisfatória várias propriedades como coeficiente de expansão térmica, distribuição de ângulos, número de coordenação, propriedades elásticas, função distribuição de pares, densidade de modos vibracionais, fator de Debye-Waller entre outros. O comportamento dos sistemas na região em que ocorrem as transições de fase também foi explorado apresentando resultados fantásticos.

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Miao, Yi. "Shape-Dependent Molecular Recognition of Specific Sequences of DNA by Heterocyclic Cations." Digital Archive @ GSU, 2006. http://digitalarchive.gsu.edu/chemistry_diss/4.

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SHAPE-DEPENDENT MOLECULAR RECOGNITION OF SPECIFIC SEQUENCES OF DNA BY HETEROCYCLIC CATIONS by YI MIAO Under the Direction of Dr. W. David Wilson ABSTRACT DB921 and DB911 are biphenyl-benzimidazole-diamidine isomers with a central para- and meta-substituted phenyl group, respectively. Unexpectedly, linear DB921 has much stronger binding affinity with DNA than its curved isomer, DB911. This is quite surprising and intriguing since DB911 has the classical curved shape generally required for strong minor groove binding while DB921 clearly does not match the groove shape. Several biophysical techniques including thermal melting (Tm), circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) have been utilized to investigate the interactions between these compounds and DNA. The structure of the DB921-DNA complex reveals that DB921 binds to DNA with a reduced twist of the biphenyl for better fit of DB921 into the minor groove. A bound water molecule complements the curvature of DB921 and contributes for tight binding by forming H-bonds with both DNA and DB921. Structure-affinity relationship studies of a series of DB921 analogs show that the benzimidazole group is one of the key groups of DB921 for its strong binding to the minor groove. Thermodynamic studies show that the stronger binding of DB921 is due to a more favorable binding enthalpy compared to DB911 even though the complex formation with DNA for these compounds are all predominantly entropically driven. DB921 also has more negative heat capacity change than DB911. The initial studies of inhibition of the interaction between an AT hook peptide of HMGA proteins and its target DNA by a set of diamidine AT-minor groove binders using biosensor-SPR technique show that the inhibitory ranking order is consistent with that of binding affinity and linear-shaped DB921 still has excellent inhibitory effects. These heterocyclic cations rapidly inhibit the binding of DBD2 peptide to the DNA and may only block the specific AT binding of the peptide without hindering the non-specific binding interaction. The results of this project have shown that DB921 represents a new novel effective minor groove binder that does not fit the traditional model and is a potential inhibitor for DNA/protein complexes. INDEX WORDS: Molecular recognition, DNA binding, Minor groove binding, Linear shape, Compound curvature, Binding affinity, Binding kinetics, Thermodynamics, Surface plasmon resonance, Isothermal titration calorimetry, Inhibition

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Hamid, Ahmed. "SOLVATION OF ORGANIC CATIONS IN THE GAS PHASE AND WITHIN MOLECULAR CLUSTERS." VCU Scholars Compass, 2012. http://scholarscompass.vcu.edu/etd/323.

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The role of the solvent in ionic and ion-molecule interactions is of fundamental importance in kinetics and thermodynamics of solution chemistry. However, the study of the ionic interactions in the presence of a large number of solvent molecules is very challenging. Therefore, the gas-phase is the appropriate medium to study such reactions on a molecular level where the ion-solvent interaction can be examined by studying ions surrounded with a cluster of solvent molecules in the complete absence of the any interference caused by the bulk of the solvent. In nature, organic ions can form hydrogen bonds with solvents. An insight into basic molecular interactions is required to be extracted from the gas phase energies and structures of the solvated organic ions. Therefore, the stepwise hydration experiments of benzene.+, C3H3+, acetylene.+, pyridine.+, 2-fluoropyridine.+, phenyl acetylene.+ and acetylene dimer.+ have been investigated using quadrupole mass-selected ion mobility mass spectrometer. Thus, these systems can be considered as prototypical models for understanding the molecular aspects leading to hydrophobic hydration in the condensed phase. Two routes of the investigation of ion-molecule interactions are considered in this dissertation. The first route is concerned with injecting the same ion into various solvents to study the nature and strength of the ion-solvent interactions when protonated pyrimidine cation interacts with water, methanol and acetonitrile molecules. Association and proton transfer reactions were observed. On the other hand, the second route involves the injection of various ions into the same solvent where the interactions of hydrogen cyanide (HCN) molecules with different ions. Benzene, phenyl acetylene, pyridine, protonated pyridine, and pyrimidine ions were investigated. All the investigated ions exhibited hydrogen bonding with the hydrogen cyanide molecules with variable strength depending on the charge distribution on the specified ion as well as the nature of interaction. Additionally, ion mobility structural methods were utilized to investigate structures of binary clusters formed by supersonic expansion of mixed vapors. The structures can be identified by comparing the experimentally measured collision cross section values with those predicted from DFT computations.

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Aylward, Susan Margaret. "New acyclic and macrocyclic ligands for the selective complexation of Groups I and II metal cations." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282395.

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49

Chanajaree, Rungroj. "The Motions of Guest Water Molecules and Cations in Chabazite." Doctoral thesis, Universitätsbibliothek Leipzig, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-68772.

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The translational self-diffusion, the librations, and the reorientational motions of guest water molecules in the zeolite chabazite are examined by Molecular Dynamics (MD) computer simulations at different temperatures and loadings, including at room temperature, at which the experiments are carried out. Satisfactory agreement is found between the computed and measured translational self-diffusion coefficients. It is, however, furthermore found that the way in which the long-range electrostatic interactions are computed has an effect on the self-diffusion at high loadings and temperatures. The spectral densities of the librational motions of water are found to be similar to those in aqueous salt solutions. The reorientations of the water molecules, on the other hand, are much slower than in the liquids, and very anisotropic. The vector in direction of the molecular dipole moment reorients only very slowly, at the time scale of the simulations, due to the attraction to the almost immobile Ca++-ions and the walls of the zeolite. The other two vectors seem to undergo jump-reorientations rather than reorientations by a diffusion process. Hyper dynamics boost potential method has been applied to the MD simulations to estimate the self-diffusion coefficients of Ca++ ions in dehydrated chabazite. Because of our system is very complicated, the self-diffusion of Ca++ ions can only be roughly estimated. The Ca++ ions diffusion is small enough to confirm that the cation motion can be neglected in the normal MD simulation.

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Lecureur-Rolland, Valérie. "Expression, regulation et activite dans les cellules hepatiques de deux transporteurs membranaires de molecules cationiques : la p-glycoproteine et le transporteur de cations organiques (oct1)." Paris 5, 1997. http://www.theses.fr/1997PA05N100.

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