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Dissertations / Theses on the topic 'Intermolecular interactions'
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1
Randall, Karen L. "Studies of intermolecular interactions." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0014/NQ28043.pdf.
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Hurst, G. J. B. "Intermolecular interactions by perturbation theory." Thesis, University of Cambridge, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356653.
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Clark, Jane Northen. "Intermolecular interactions in polymer blends." Thesis, Imperial College London, 1990. http://hdl.handle.net/10044/1/47811.
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Varley, Lisa. "Intermolecular interactions : quantification and applications." Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/2739/.
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This thesis deals with the nature of fundamental intermolecular interactions and the ways in which they can be exploited using supramolecular chemistry. Three separate studies have been undertaken in order to explore and quantify different types of electrostatic interactions. Chapter 2 describes an investigation into the nature of hydrogen bonding interactions between charged species and well-defined neutral hosts, in order to quantify their hydrogen bonding strength on an already established scale. The importance of metal-ligand interactions in self-assembly is documented in Chapter 3, where the synthesis of functional supramolecules is described and their self-assembly in the presence of a bidentate ligand is investigated. Finally, Chapter 4 describes the use of calixarene-porphyrin conjugates in gas-sensing devices, showing how a handle on the design and synthesis of supramolecules and an understanding of their basic interactions can provide a useful application. The detailed background literature relating to the project will be described as an introduction to each chapter; this chapter provides a general introduction to the field of supramolecular chemistry and an overview of key advances that have been made since its inception.
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Moujaes, Elie A. "Intermolecular vibronic interactions in fullerene anions." Thesis, University of Nottingham, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438359.
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Hudson, Amanda Gayle. "Characterization of Intermolecular Interactions in Nanostructured Materials." Diss., Virginia Tech, 2015. http://hdl.handle.net/10919/77855.
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Advanced analytical techniques were utilized to investigate the intermolecular forces in several nanostructured materials. Techniques including, but not limited to, isothermal titration calorimetry (ITC), variable temperature Fourier transform infrared (FTIR) spectroscopy, and ultraviolet-visible (UV-Vis) thermal curves were used to study the fundamental interactions present in various nanomaterials, and to further probe the influence of these interactions on the overall behavior of the material. The areas of focus included self-assembly of surfactant micelles, polycation complexation of DNA, and temperature-dependent hydrogen bonding in polymeric systems.
ITC was successfully used to determine the low critical micelle concentration (CMC) for a novel gemini surfactant with limited water solubility. CMCs were measured at decreasing methanol molar fractions (xMeOH) in water and the resulting linear relationship between CMC and methanol concentration was used to mathematically extrapolate to a predicted CMC at xMeOH = 0. Using this technique, the CMC value for the novel gemini surfactant was predicted to be 0.037 ± 0.004 mM. This extrapolation technique was also validated with surfactant standards.
ITC was also used to investigate the binding thermodynamics of polyplex formation with polycations and DNA. The imidazolium-containing and trehalose-based polycations were both found to have endothermic, entropically driven binding with DNA, while the adenine-containing polycation exhibited exothermic DNA binding. In addition, ITC was also used to confirm the stoichiometric binding ratio of linear polyethylenimine and DNA polyplexes as determined by a novel NMR method. Dynamic light scattering (DLS) and zeta potential measurements were also performed to determine the size and surface charge of polyplexes. Circular dichroism (CD) and FTIR spectroscopies provided information regarding the structural changes that may occur in the DNA upon complexation with polymers. UV-Vis thermal curves indicated that polyplexes exhibit a greater thermal stability than DNA by itself.
Variable temperature FTIR spectroscopy was used to quantitatively compare the hydrogen bonding behavior of multi-walled carbon nanotube (MWCNT)-polyurethane composites. Spectra were collected from 35 to 185 deg C for samples containing various weight percent loadings of MWCNTs with different hydrogen bonding surface functionalities. Peak fitting analysis was performed in the carbonyl-stretching region for each sample, and the hydrogen-bonding index (Rindex) was reported. Rindex values were used to quantitatively compare all of the composite samples in regards to temperature effects, weight percent loadings of MWCNTs, and the different functionalizations. In general, higher weight percent loadings of the MWCNTs resulted in greater Rindex values and increased hydrogen bond dissociation temperatures. In addition, at 5 and 10 wt% loadings the initial Rindex values displayed a trend that tracked well with the increasing hydrogen bonding capacity of the various surface functionalities.Ph. D.
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Inglefield, Jr David Lott. "Tailoring Intermolecular Interactions for High-Performance Nanocomposites." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/64411.
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Acid oxidation of multi-walled carbon nanotubes (MWCNTs) introduced carboxylic acid sites onto the MWCNT surface, which permitted further functionalization. Derivatization of carboxylic acid sites yielded amide-amine and amide-urea functionalized MWCNTs from oxidized precursors. Conventional MWCNT characterization techniques including X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), and Raman spectroscopy supported successful MWCNT functionalization. Incorporation of MWCNTs functionalized with hydrogen bonding groups into a segmented polyurethane matrix led to an increase in mechanical properties at optimized MWCNT loadings, in contrast with non-functionalized MWCNTs that resulted in mechanical property decreases across all loadings. Dynamic mechanical analysis (DMA) demonstrated an increase in the polyurethane-MWCNT composite flow temperature with increasing hydrogen bonding MWCNT incorporation, as opposed to non-functionalized MWCNT composites which displayed no significant change in flow temperature. Variable temperature Fourier transform infrared spectroscopy (VT FT-IR) probed temperature-dependent hydrogen bonding in the polyurethane-MWCNT composites and revealed a significant impact on composite hydrogen bonding interactions upon MWCNT incorporation, which was amplified in composites formed using hydrogen bonding functionalized MWCNTs.
Acid oxidation of carbon nanohorns (CNHs) yielded carboxylic acid functionalized CNHs, providing sites for further reaction with histamine to afford histamine-functionalized CNHs (His-CNHs). Raman spectroscopy, XPS and TGA confirmed successful functionalization.
Transmission electron microscopy (TEM) demonstrated that His-CNHs efficiently complex quantum dots (QDs) through imidazole-Zn interactions. Combination of His-CNHs, QDs, and a poly(oligo-(ethylene glycol9) methyl ether methacrylate)-block-poly(4-vinyl imidazole) copolymer using an interfacial complexation technique afforded stable ternary nanocomplexes with average hydrodynamic diameters under 100 nm. These ternary nanocomplexes represent promising materials for photothermal cancer theranostics due to their size and stability.
The efficient reaction of 2-isocyanatoethyl methacrylate with amines afforded urea-containing methacrylic monomers, where the amine-derived pendant groups determined the polymer Tg. Reversible addition-fragmentation chain-transfer (RAFT) polymerization enabled the synthesis of ABA triblock copolymers with urea-containing methacrylic outer blocks and poly(2-ethylhexyl methacrylate) inner blocks. These ABA triblocks copolymers displayed composition dependent phase-separated morphologies and desirable mechanical properties. The urea-containing polymers efficiently complexed gold nanoparticles through urea-gold interactions. Furthermore, urea-containing methacrylic polymers served as a useful matrix for incorporation of silica-coated upconverting nanoparticles, affording upconverting nanoparticle composite films.The novel ionene monomer N1,N2-bis(3-(dimethylamino)propyl)oxalamide permitted synthesis of novel oxalamide-containing ammonium ionenes. The hydrogen bonding, charge density, and counter anion tuned the ionene mechanical properties. The ionene structure also influenced water uptake and conductivity. The differences in physical properties correlated well with the morphology observed in small-angle X-ray scattering. The oxalamide-containing ionenes greatly enhance mechanical properties compared to typical ammonium ionenes, and further expand the library of ionene polymers.Ph. D.
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Inglefield, David Lott Jr. "Tailoring Intermolecular Interactions for High-Performance Nanocomposites." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/64411.
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Acid oxidation of multi-walled carbon nanotubes (MWCNTs) introduced carboxylic acid sites onto the MWCNT surface, which permitted further functionalization. Derivatization of carboxylic acid sites yielded amide-amine and amide-urea functionalized MWCNTs from oxidized precursors. Conventional MWCNT characterization techniques including X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), and Raman spectroscopy supported successful MWCNT functionalization. Incorporation of MWCNTs functionalized with hydrogen bonding groups into a segmented polyurethane matrix led to an increase in mechanical properties at optimized MWCNT loadings, in contrast with non-functionalized MWCNTs that resulted in mechanical property decreases across all loadings. Dynamic mechanical analysis (DMA) demonstrated an increase in the polyurethane-MWCNT composite flow temperature with increasing hydrogen bonding MWCNT incorporation, as opposed to non-functionalized MWCNT composites which displayed no significant change in flow temperature. Variable temperature Fourier transform infrared spectroscopy (VT FT-IR) probed temperature-dependent hydrogen bonding in the polyurethane-MWCNT composites and revealed a significant impact on composite hydrogen bonding interactions upon MWCNT incorporation, which was amplified in composites formed using hydrogen bonding functionalized MWCNTs.
Acid oxidation of carbon nanohorns (CNHs) yielded carboxylic acid functionalized CNHs, providing sites for further reaction with histamine to afford histamine-functionalized CNHs (His-CNHs). Raman spectroscopy, XPS and TGA confirmed successful functionalization.
Transmission electron microscopy (TEM) demonstrated that His-CNHs efficiently complex quantum dots (QDs) through imidazole-Zn interactions. Combination of His-CNHs, QDs, and a poly(oligo-(ethylene glycol9) methyl ether methacrylate)-block-poly(4-vinyl imidazole) copolymer using an interfacial complexation technique afforded stable ternary nanocomplexes with average hydrodynamic diameters under 100 nm. These ternary nanocomplexes represent promising materials for photothermal cancer theranostics due to their size and stability.
The efficient reaction of 2-isocyanatoethyl methacrylate with amines afforded urea-containing methacrylic monomers, where the amine-derived pendant groups determined the polymer Tg. Reversible addition-fragmentation chain-transfer (RAFT) polymerization enabled the synthesis of ABA triblock copolymers with urea-containing methacrylic outer blocks and poly(2-ethylhexyl methacrylate) inner blocks. These ABA triblocks copolymers displayed composition dependent phase-separated morphologies and desirable mechanical properties. The urea-containing polymers efficiently complexed gold nanoparticles through urea-gold interactions. Furthermore, urea-containing methacrylic polymers served as a useful matrix for incorporation of silica-coated upconverting nanoparticles, affording upconverting nanoparticle composite films.The novel ionene monomer N1,N2-bis(3-(dimethylamino)propyl)oxalamide permitted synthesis of novel oxalamide-containing ammonium ionenes. The hydrogen bonding, charge density, and counter anion tuned the ionene mechanical properties. The ionene structure also influenced water uptake and conductivity. The differences in physical properties correlated well with the morphology observed in small-angle X-ray scattering. The oxalamide-containing ionenes greatly enhance mechanical properties compared to typical ammonium ionenes, and further expand the library of ionene polymers.Ph. D.
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Robertson, Katherine N. "Intermolecular interactions in a series of organoammonium tetraphenylborates." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ66644.pdf.
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Fortin, Anouk S. "Intra- and intermolecular interactions governing Pax-3 function." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=37617.
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Pax-3 is a transcription factors important in normal embryonic development, as highlighted by its mutation in independent alleles of the Splotch mouse mutant and human Waardenburg syndrome, both characterized by pigmentary disturbances in the heterozygous state and limb muscle defects in the homozygotes. Pax-3 contains two structurally independent DNA-binding domains, a paired domain and a homeodomain. Through the analysis of a number of naturally occurring mutations, we have shown that both DNA-binding domains are functionally interdependent, as independent mutations in either domain can affect the DNA-binding activity of the other. In support of this finding, modeling the deleterious mutations into the three dimensional structure of the paired domain suggests that a series of consecutive phosphate contacts are essential for DNA-binding by both the paired domain and homeodomain of Pax-3. In addition, the paired domain can regulate the DNA-binding specificity and dimerization potential of the homeodomain and we have exploited the possibility to transfer this effect to a heterologous homeodomain to identify the protein segments involved in this functional interaction. Characterization of a series of chimeric proteins containing stepwise deletions within the paired domain provided two key findings: (i) the C-terminal subdomain of the paired domain does not play a major role in the regulation of the homeodomain DNA-binding and (ii) the N-terminal subdomain and, in particular, the second alpha-helix are essential for the modulation of homeodomain DNA-binding. In addition to intermolecular interactions, the functional association with other transcription factors can also modulate Pax-3 target gene selection and regulation. We found that Pax-3 can recruit PEA3, a member of the ETS family, to form a ternary complex with DNA sequences containing either a paired domain or homeodomain recognition site and a sub-optimal Ets site to which PEA3 normally does not bind. We have
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Page, Christopher Samuel. "On non-classical intermolecular interactions and chiral recognition." Thesis, Imperial College London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.287722.
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Odendal, James Arthur. "Investigating intermolecular interactions motifs in ammonium carboxylate salts." Thesis, Stellenbosch : University of Stellenbosch, 2009. http://hdl.handle.net/10019.1/2965.
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Thesis (MSc (Chemistry and Polymer Science))--University of Stellenbosch, 2009.ENGLISH ABSTRACT: This thesis reports an in-depth investigation of the intermolecular interaction motifs in secondary, primary and ammonium carboxylate salts. The investigation was conducted using the Cambridge Structural Database (CSD), together with a systematic steric-specific experimental study. The tendency in the literature has been to analyse organic salt crystal structures in terms of hydrogen bonding patterns, almost ignoring cation-anion interactions. This study focuses on the cation-anion interactions in secondary, primary and ammonium carboxylate salts, which have a direct effect on the formation of specific structural motifs. The ideas of ring-stacking and ring-laddering, which arise from the tendency of cations and anions to arrange themselves so as to maximise electrostatic interactions, have been applied to ammonium carboxylate salts. An extensive survey of organic ammonium carboxylate salt structures in the CSD has been carried out. The structural motifs in ammonium carboxylates were investigated, and a set of predictive rules for the pattern of intermolecular interactions in these salts was developed. Using these results, the formation of ring-stacking or ring-laddering in primary ammonium carboxylate salts can be predicted. The results from the CSD survey are discussed in Chapter 3. An experimental study has been carried out, which complements the results obtained from the CSD survey. The experimental study formed 19 novel ammonium carboxylate salts, of which 2 formed hydrates and 2 co-crystals of salts. The experimental results confirm what was found in the CSD survey, and this is discussed in Chapter 4. This study has found that the principle of ring-stacking and ring-laddering can be applied in a general form to the crystal structures of organic ammonium carboxylate salts. The size of the cation and the anion in these salts has a significant effect on the formation of structural motifs in the solid state. Interactions between cation and anion substituents also play an important role in the formation of particular structural motifs in ammonium carboxylate salts.
AFRIKAANSE OPSOMMING: In hierdie tesis word die intermolekulêre interaksie motiewe in die sekondêre, primêre en ammonium karbosilaat soute in-diepte ondersoek. Die studie is gedoen met behulp van die Cambridge Strukturele Databasis (CSD), saam met ‟n sistematiese steriesspesifieke eksperimentele studie. Die neiging in die literatuur is om organiese sout kristal strukture in terme van waterstofbindings patrone te analiseer sonder om katioon-anioon interaksies in ag te neem. Die studie fokus juis op hierdie katioon-anioon interaksies tussen sekondêre, primêre en ammonium karbosilaat soute wat ‟n direkte effek het op die vorming van spesifieke strukturele motiewe naamlik „ring-stacking‟ en „ring-laddering‟ wat hul oorsprong kry vanaf die neiging van katione en anione om hulself op so ‟n wyse te rangskik sodat die elektrostatiese interaksies ‟n maksimum kan bereik, op die ammonium karboksilaat soute. ‟n Volledige ondersoek van ammonium karboksilaat soute in die CSD is gedoen. Die strukturele motiewe in ammonium karboksilaat is ondersoek, en ‟n stel reels wat die patrone van intermolekulêre interaksies in hierdie soute voorspelis ontwikkel. Hierdie resultate kan gebruik word om die vorming van „ring-stacking‟ en „ring-laddering‟ in primêre ammonium karbosilaat soute te voorspel. Die resultate van die CSD ondersoek word bespreek in Hoofstuk 3. ‟n Eksperimentele studie is uitgevoer en die resultate hiervan komplimenteer die resultate van die CSD ondersoek. In die eksperimentele studie is 19 nuwe ammonium karboksilaat soute gekristaliseer, waarvan 2 hidraat-soute en 2 ko-kristal-van-soute is. Die eksperimentele resultate bevestig die bevindings van die CSD ondersoek, en dit word bespreek in Hoofstuk 4. Hierdie studie het gevind dat die beginsel van „ring-stacking‟ en „ring-laddering‟ kan in „n algemene vorm in die kristal strukture van organiese ammonium karboksilaat soute toegepas word. Die grootte van die katioon en anion in hierdie soute het ‟n beduidende effek op die vorming van strukturele motiewe in die vaste toestand. Interaksie tussen die katioon en anioon substituente speel „n belangrike rol in die vorming van spesifieke motiewe in ammonium karbosilaat soute.
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Araújo, Ana Catarina Fernandes. "Molecular modeling of intermolecular interactions in acid hydrates." Master's thesis, Universidade de Aveiro, 2012. http://hdl.handle.net/10773/10947.
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Mestrado em QuímicaEsta dissertação explora o mundo nanoscópico de pequenos agregados onde as pontes de hidrogénio têm um papel preponderantes usando métodos quânticos ab-initio. No capítulo introdutório, a área da química computacional é apresentada e algumas noções teóricas referentes aos métodos ab-initio, discutidas. No Capítulo 2, o desempenho de vários níveis de teoria é avaliado através do estudo de pequenos agregados de água. O capítulo 3 discute a influência dos critérios de optimização no resultado deste processo, alertando para erros comuns. No Capítulo 4, hidratos gasosos de ácido trifluoroacético (TFA), nas formas dissociada e não-dissociada, são apresentados. Um número mínimo de 4 moléculas de água é necessário para induzir a transferência do protão do TFA para a rede de moléculas de água adjacente . No entanto, 5 moléculas de água são necessárias para que o agregado dissociado se torne mais estável que o seu análogo não dissociado. O Capítulo 5 propõe um novo esquema para o cálculo ab-initio de valores de pKa. Este esquema serve-se de hidratos de ácido microsolvatado, nas formas dissociada e não dissociada, em modelo de solvatação contínuo, para calcular a energia livre de dissociação em solução. Para o conjunto de espécies testadas, incluindo 10 ácidos carboxílicos, 1 amina e 2 aminoácidos, o erro médio absoluto é 1.11, o declive experimental 1.2 e o coeficiente de correlacção 0.92, o que indica um nível de exactidão aceitável.
This dissertation concerns the study of small hydrogen bonded systems through the use of quantum mechanical ab-initio methods. In the introductory chapter, the field of computational chemistry is presented and some basic theoretical notions concerning ab-initio methods are discussed. In Chapter 2, the performance of various levels of theory is assessed through the study of small water clusters. Chapter 3 discusses the influence of optimization criteria in the outcome of the optimization procedure, warning against common pitfalls. In Chapter 4, gas-phase hydrates of trifluoroacetic acid (TFA), in both dissociated and undissociated forms, are presented. A minimum of 4 water molecules is necessary to induce proton transfer from TFA to the neighboring water molecule network. However, 5 water molecules are needed to render the dissociated hydrate more stable than its undissociated counterpart. Chapter 5 proposes a new scheme for the ab-initio calculation of pKa values. It uses microsolvated acid hydrates, in both dissociated and undissociated forms, within a continuum solvation model, to calculate the dissociation free energy in solution. For the data set used, including 10 carboxylic acids, 1 amine and 2 aminoacids, the mean usigned error (MUE) of calculated pKa values is 1.11, the experimental slope 1.2 and the correlation 0.92, which denotes a reasonable level of accuracy.
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Allen, Stephanie. "The study of biomolecular interactions using scanning probe microscopy." Thesis, University of Nottingham, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363596.
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Zanbot, Dina. "Dynamics, Intermolecular Interactions, and Organization of Transmembrane β-Peptides." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2017. http://hdl.handle.net/11858/00-1735-0000-002E-E33F-1.
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Dejaegere, Annick P. "Experimental and theoretical study of intermolecular interactions in solution." Doctoral thesis, Universite Libre de Bruxelles, 1989. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/213264.
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Omnes, Laurent. "Towards the biaxial nematic phase via specific intermolecular interactions." Thesis, University of Exeter, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368368.
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Vazquez, Montelongo Erik Antonio. "Computational Study of Intermolecular Interactions in Complex Chemical Systems." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1703283/.
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This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).
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Paulo, Joao A. "Exploring intramolecular and intermolecular interactions of -bungarotoxin binding proteins." View abstract/electronic edition; access limited to Brown University users, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3318348.
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SCUDIERI, PAOLO. "Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity." Doctoral thesis, Università degli studi di Genova, 2018. http://hdl.handle.net/11567/929402.
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TMEM16A e TMEM16B sono proteine di membrana con funzione di canali
del cloruro attivati da calcio. Attraverso la generazione di canali chimerici, e in
particolare, sostituendo la regione carbossi-terminale di TMEM16A con la regione
equivalente di TMEM16B, sono stati ottenuti dei canali dotati di una maggiore
attività. Il progressivo accorciamento della regione chimerica ha permesso di
restringere il “dominio attivante” a una corta sequenza di 14 aminoacidi localizzata
vicino all’ultimo dominio transmembrana e ha generato proteine-canale TMEM16A
dotate di un’attività molto alta anche a concentrazioni basse di calcio intracellulare.
Per chiarire il meccanismo molecolare alla base di questo effetto, sono stati
eseguiti esperimenti basati sulla generazione di doppie chimere, Forster resonance
Energy transfer e cross-linking intermolecolare. Inoltre, è stato generato un
modello tridimensionale teorico di TMEM16A basato sulla struttura di una proteina
TMEM16 del fungo Nectria haematococca. I risultati ottenuti indicano che
l’aumentata attività nei canali chimerici è causata da un’alterazione dell’interazione
tra il carbossi-terminale e la prima ansa intracellulare di TMEM16A.
L’identificazione di piccole molecole farmacologiche in grado di mimare
questa perturbazione potrebbe rappresentare la base di un approccio farmacologico
volto a stimolare il trasporto ionico TMEM16A-dipendente. L’attivazione
farmacologica di TMEM16A potrebbe essere utile per stimolare la secrezione
epiteliale nelle vie aeree, un effetto potenzialmente benefico in patologie quali la
fibrosi cistica e altre malattie ostruttive croniche dell’apparato respiratorio
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Johnson, Erin R. "A density-functional theory including dispersion interactions." Thesis, Kingston, Ont. : [s.n.], 2007. http://hdl.handle.net/1974/926.
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Alexopoulos, Eftichia. "Crystallographic and modeling studies of intermolecular interactions of biological interest." Doctoral thesis, [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972659137.
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Schultheiss, Nathan C. "Balancing intermolecular interactions in the design and synthesis of supermolecules." Diss., Manhattan, Kan. : Kansas State University, 2007. http://hdl.handle.net/2097/264.
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Bellamy, Dena. "Intermolecular interactions in transition metal complexes and analogous organic species." Thesis, University of Bristol, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.389380.
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Panova, Stanislava. "NMR approaches to understanding intramolecular and intermolecular interactions in proteins." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/nmr-approaches-to-understanding-intramolecular-and-intermolecular-interactions-in-proteins(95a44c16-fd44-4909-8ee2-435f574d2970).html.
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Inhibition of the intrinsically disordered proteins (IDP) is a recognized issue in drug research. Standard approaches, based on key-lock model, cannot be used in the absence of rigid structure and defined active site. Here a basic helix-loop-helix leucine zipper (bHLHZip) domain of c-Myc was studied, which is intrinsically disordered and prone to aggregation. Chemical denaturation of proteins is a widely accepted technique to study protein folding, but here this methodology was applied to IDP, observing its effect on the structural ensemble of c-Myc by NMR spectroscopy. Nonlinear chemical shift changes indicated cooperative unfolding of the helical structure of the part of the leucine zipper domain in parallel with the melting of the N-terminal helix. Paramagnetic relaxation enhancement (PRE) was used to probe long-range structure and revealed presence of long-range contacts. The following search for inhibitors can be directed to the search for ligands, locking c-Myc in its more compact conformation. Protein self-association is a problem typical for IDPs and intrinsic process for all proteins at high concentrations. It leads to increased viscosity, gelation and possible precipitation, which cause problems in protein manufacturing, stability and delivery. If protein drugs require high dosing, special approaches are needed. At high concentrations proteins experience conditions close to the crystal state, therefore interactions in solution could potentially coincide with crystal lattice contacts. A range of diverse methods is used to study this process, but the complexity of the mechanism makes it hard to build a reliable model. Here, the self-association of streptococcal Protein G (PrtG) was studied using Nuclear Magnetic Resonance (NMR) spectroscopy in solution. The properties of protein-protein interactions at high concentration, up to ~ 160 mg/ml, were studied at residue-level resolution. Residue specific information on protein dynamics was obtained using 15N relaxation measurements. The experiments were carried out at multiple concentrations. Variation in the rotational correlation time over these concentrations showed changes in the protein dynamics, which indicated weak protein-protein interactions occurring in solution. Pulsed-field gradient NMR spectroscopy was used to monitor translational diffusion coefficients in order to estimate the degree of protein self-association. Oligomer formation was also monitored by looking at variations in 1H and 15N amide chemical shifts. Better understanding of protein self-association mechanisms under different conditions could assist in developing methods to reduce the level of reversible protein self-association in solution at high protein concentrations.
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Lane, Jordan Samuel. "Soluble modulators of intermolecular interactions in proteins and lipid rafts." Thesis, University of Nottingham, 2018. http://eprints.nottingham.ac.uk/49874/.
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The nonspecific binding of proteins to various biological and non-biological surfaces has limited the potential of several detection techniques such as surface plasmon resonance (SPR), Luminex and ELISA (among others). Plasma proteins have been shown to decrease the sensitivity of instruments when working with complex fluids such as blood samples. This study examines the binding properties of several plasma proteins to a range of surfaces and utilises reagents in the media to eliminate the nonspecific binding of the plasma proteins. This has created a set of conditions that can reduce the nonspecific binding interaction, without affecting the specific interactions which the various techniques measure. These mechanisms were then applied to the assembly/disassembly of membrane microdomains. Membrane microdomains have been shown to be affected by from several factors such as acyl-chain length and temperature. This study demonstrates how reagents in the media can affect the assembly of these domains. We proposed a novel mechanism for the regulation of the domains, in which the reagents alter the intermolecular interactions between lipid head groups by altering the water network around these domains to promote domain assembly. These results that could have significant ramifications for the functional characterisation of membrane microdomains and the proteins that are known to associate with them. Finally, membrane binding affinity and kinetics of different polypeptides with various lipid membrane composition were characterised and resultant microdomains were monitored. Demonstrating how the previously uncontrolled, soluble factors in a model system can control the intermolecular interactions that occur in the system that is being measured.
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Russ, Jennifer Lynn. "Studies of Solution Paramagnetic-Substrate Nuclear and Electron Intermolecular Interactions." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/27050.
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Advanced nuclear and electron magnetic resonance techniques (i.e. nuclear magnetic resonance (NMR), dynamic nuclear polarization (DNP), and magnetic resonance imaging (MRI)) were used to study the attitude and dynamics of TEMPO (2,2,6,6-tetramethylpiperidinyloxy)-substrate systems and the relaxivity properties of water-soluble trimetallic nitride template functionalized endohedral metallofullerenes (TNT-fMF). The attitude and average distance of interaction for each TEMPO-substrate system was determined from comparing density functional theory (DFT) calculation results with experimental hyperfine coupling constants leading to an improved understanding of solution dynamics. The short-lived solvent-solute interactions of the TEMPO-substrate molecules, such as transient complex formation, are governed by weak hydrogen-bonding interactions. The collisions in solution were explained by determining the favored orientations of the two molecules interacting using calculated relative energy minima and reproducibility of the experimental results by the calculated coupling constants.
Water-soluble TNT-fMFs are studied as candidates for the next generation MRI contrast agents as diagnostic agents and also as possible therapeutic agents to kill cancer cells and decrease tumors. The TNT-fMFs are being studied as part of a multi-modal platform dependent upon which metal atoms are encapsulated inside: Gd â MRI contrast agent (diagnostic), Lu and Ho â radio labeled for use as a therapeutic agent, Tb â fluorescence, and Lu â x-ray contrast. The current commercial MRI contrast agent, OmniscanTM, contains one gadolinium atom; however, the metal is complexed to, not encapsulated in, the molecule. TNT-fMFs fully encapsulate three metal atoms to ensure the patient does not run the risk of metal poisoning. The r1 and r2 relaxivities of TNT-fMFs containing either Gd, Lu, Ho, or Sc metals were measured at 0.35T. The data for the Gd containing TNT-fMFs indicated the metallofullerene has significantly higher relaxivities than OmniscanTM, and can be the next generation MRI contrast agent. The Ho containing species has a high r2/r1 ratio compared to the other samples showing it is a potential T2 agent, and has therapeutic capabilities.Ph. D.
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Mehra, Nitin. "Thermal Conduction in Polymer Based Materials by Engineering Intermolecular Interactions." University of Akron / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=akron1578202939238852.
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Kang, Myungshim. "Molecular dynamics simulations and theory of intermolecular interactions in solutions." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1282.
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Vitorica, Inigo. "Solid state supramolecular chemistry : gas-solid reactions and intermolecular interactions." Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/3926/.
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Oliveira, de Figueiredo Martins Ana Rita. "Effect of intermolecular interactions on the viscoelastic behavior of polyamides." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSE1034/document.
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Les polyamides sont des thermoplastiques techniques qui présentent de bonnes propriétés mécaniques et barrières. Le comportement viscoélastique complet des polyamides est rarement décrit dans la littérature à cause de la présence d'une phase cristalline et à l'instabilité thermique de ces polymères.Dans une première partie, le comportement rhéologique de polyamides amorphes PA 6I avec différentes masses molaires a été étudié. L'augmentation de la masse molaire se traduit par l'apparition d'un plateau caoutchoutique et le décalage du temps de relaxation terminal vers les plus basses fréquences, en accord avec les modèles de Rouse et de reptation. Des interactions ioniques ont été ajoutées au PA 6I en copolymérisant les mêmes monomères avec différents acides isophtaliques substitués, avec des taux de groupements ioniques de 5 à 20 mol%, ce qui entraîne une augmentation de la température de transition vitreuse de 10 à 40°C. Les courbes maîtresses des PA 6I et des copolyamides substitués non enchevêtrés se superposent dans toute la gamme de fréquences en utilisant une température de référence appropriée, proche mais non strictement identique à Tg. Les groupements ioniques ont un effet sur la fragilité dynamique, c'est-à-dire sur la variation en température de la réponse rhéologique près de Tg. Le modèle de Rouse décrit correctement la réponse rhéologique des polyamides non enchevêtrés, montrant que les interactions ioniques n'ont pas d'effet sur la viscoélasticité de ces matériaux. Les polyamides enchevêtrés suivent le modèle de la reptation. La masse entre enchevêtrements augmente avec l'ajout de groupements ioniques dû à une augmentation de la rigidité de la chaîne. La diffusion des rayons-X aux petits angles montre qu'il n'y a pas de ségrégation de domaines ioniques dans les copolyamides non enchevêtrés et une faible ségrégation dans les copolyamides enchevêtrés. L'ajout de liaisons hydrogènes plus fortes se traduit par l'augmentation de la masse entre enchevêtrements et de la Tg sans aucune modification significative dans l'allure des courbes maîtresses qui restent bien décrites par le modèle de Rouse. L'effet des groupements ioniques sur la dynamique à l'état solide (au-dessous de Tg) a été étudié par spectroscopie diélectrique. Les groupements ioniques n'ont pas d'effet sur les relaxations secondaires des polyamides, tandis que la relaxation alpha est décalée comme la Tg mesurée par DSC. Aucune différence n'a été observée entre les copolyamides ioniques et le PA 6I lors de tests de vieillissement physique, démontrant que les groupements ioniques n'introduisent pas d'hétérogénéités dynamiquesPolyamides are engineering thermoplastics which exhibit good mechanical and barrier properties. However, the viscoelastic behavior over the complete range of polyamide relaxation is a topic rarely mentioned in the literature due to the presence of a crystalline phase and lack of thermal stability.The rheological behavior of amorphous PA 6I with increasing molecular weight was studied. As molecular weight increases, a clear rubbery plateau appears and the longest relaxation time is shifted to lower frequencies, as expected by the Rouse and reptation models.Interactions were added to the PA by copolymerizing PA 6I’s monomers with different substituted isophthalic acids. Ionic copolyamides were synthesized in molar fractions from 5 to 20 mol%, inciting an increase of about 10 to 40°C in the glass transition temperature. Master curves of unentangled PA 6I and substituted polyamides, with similar molecular weight, overlap in the complete frequency range using an appropriate reference temperature, which is close to, but not identical to Tg. Ionic groups have an effect on the Angell’s dynamical fragility, i.e. on the temperature variation of the rheological response close to Tg. Dynamic moduli of unentangled polyamides were fitted with Rouse model, showing no effect of hydrogen bonds or ionic groups on the shape of the rheological master curves. The molecular weight between entanglements increases for ionic copolyamides due to an increase of chain rigidity. Small-angle X-ray scattering shows that no segregation of ionic domains occurs in unentangled ionic copolyamides, while entangled copolyamides show only weak segregation.Stronger hydrogen bonding resulted in a decrease of the molecular weight between entanglements. Nevertheless no significant difference was observed in the shape of master curves, which were fitted using the Rouse model.The effect of interacting groups on the local dynamics in the solid state (below Tg) was studied by dielectric spectroscopy. Ionic groups have no effect on secondary relaxations, while alpha-relaxation is shifted accordingly to Tg. No difference was observed between ionic copolyamides and PA 6I during aging experiments, as ionic groups do not act as dynamic heterogeneities, i.e., zones where the local dynamics are heterogeneous due to different local ionic fractions
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Maloney, Andrew Gerrard Patrick. "PIXEL analysis of interactions in organic and inorganic systems." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/10478.
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The PIXEL method has been used for several years to analyse intermolecular interactions in organic crystals. The simplicity and speed of the calculations, along with the breakdown of intermolecular energies into physical contributing terms, mean that it has had a massive influence on the way organic crystal structures are interpreted. In the work done to date, the parameters required to perform a PIXEL calculation have been established for 1st, 2nd and 3rd row transition metals. Using these parameters, lattice energies of several transition metal complexes containing various chemical environments have been calculated and compared to experimental sublimation enthalpies. Straight line parameters for these results have been comparable to work by Gavezzotti, the author of the program, in testing the method for organic crystal structures. In addition to lattice energies, PIXEL gives dimer interaction energies of molecules in a crystal structure. The values of these interactions have been compared to single point DFT energy calculations. PIXEL has shown good agreement with a range of different intermolecular interactions, along with a significant saving in computer time over the higher level calculations. Aside from four empirical parameters, PIXEL requires only fundamental atomic properties such as ionisation potentials, electronegativities and van der Waals radii. For the most part, these values are obtained from standard reference tables and texts with the exception of atomic polarizabilities. This parameter is of great importance as it is used during the calculation of the dispersion term, an interaction which has a major influence on crystal packing. In previous work, atomic polarizabilities have been calculated using either the Slater-Kirkwood approximation or the Clausius-Mossotti relation. Both of these methods are rather simple, and do not account for possible changes in atomic polarizability resulting from differences in chemical environment. The Atoms in Molecules (AIM) approach has been used to attempt to obtain a range of polarizability values for atoms common to organic chemistry. It is observed that in the series of straight chained primary monoamines, Cn-H2n+3N, an alternation in melting points occurs between odd and even values of n. This alternation could be traced to differences in hydrogen-bonding and chain-packing that occur between odd and even-membered amines. Molecular interaction energy calculations were carried out using the PIXEL method, enabling quantitative energetic analysis of the packing differences. In this work, the crystal structures of the primary amines from ethylamine to decylamine were solved for the first time. All of these compounds are liquids at room temperature, so crystals were grown in situ by laser-assisted zone refinement at 10 K below their melting points. Diffraction data were then collected at 150 K. From propylamine to decylamine, all crystal structures are orthorhombic (or pseudo-orthorhomic) with the unit cell dimensions ~5 Ǻ x ~7 Ǻ x c Ǻ, where c increases with chain length. In the case of ethylamine, a phase characterised by single crystal diffraction at 180 K underwent a transition to a different phase on cooling to 150 K. The low-temperature phase was investigated using powder methods.
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Stadtmüller, Benjamin [Verfasser]. "Study of intermolecular interactions in hetero-organic thin films / Benjamin Stadtmüller." Aachen : Hochschulbibliothek der Rheinisch-Westfälischen Technischen Hochschule Aachen, 2013. http://d-nb.info/1037052323/34.
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Bardin, Julie. "Combined experimental and theoretical studies of intermolecular interactions in crystalline solids." Thesis, University of Strathclyde, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.538890.
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Clark, Jenny. "Intermolecular interactions in π-conjugated molecules : optical probes of chain conformation." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597713.
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A study of interactions between molecules of the same material was performed on a model polymer system. Regio-regular poly(3-hexylthiophene) (P3HT) self-organises into two-dimensional π-stacked lamellar structures. Although the chains pack at a distance of only 3.8Å, the resonant coulomb interaction between nearest-neighbour molecules is small, owing to large average conjugation lengths within the lamellae. When the resonant coulomb (or excitonic) interaction is smaller than the vibrational relaxation energy, the excitation is localised on a single molecule and the coupling is termed weak. Here we demonstrate that the polymer absorption and emission spectra can be comprehensively explained using a weakly interacting H-aggregate model. Using an analytic form of the model we can estimate the excitonic interaction energy from the ratio of the 0-0 and 0-1 absorbance peaks. It was found to vary between 5-30meV. We use this powerfully simple tool to determine how film micromorphology depends on processing. We find that films spun from low boiling point solvents show a decrease in crystalline quality, an increase in excitonic coupling and more amorphous regions, than films spun from high boiling point solvents. We correlate these findings with field-effect transistor characteristics to produce a model of film micro-morphology. We also demonstrate preliminary results that show that due to the aggregate nature of the primary neutral excitation, photo-induced charge generation in P3HT is due to exciton-exciton annihilation. Finally, we study the intermolecular interactions at an interface between two different molecules (a hole transporting polymer, TFB (Poly(9,9-dioctylfluorene –co-N-(4-butylphenyl)diphenylamine)) and an electron-transporting disoctic, HATNA-SC12 (Hexa-azatrinaphthylene)). Depending on the energetics of the interface between two materials, the inter-molecular state can be stabilised by either coulomb interactions (as in the case of single material interfaces) or charge-transfer interactions. In this case, we find that the charge-transfer interactions dominate and an excited-state complex, or exciplex, is formed. The exciplex is generated efficiently in light-emitting diodes, producing a pure red emission. In polymer/polymer blends efficient bulk exciton emission can occur due to endothermic transfer from the exciplex to the bulk exciton. In this system, however the exciplex is stable at the interface, acting as an energy bottleneck with inefficient transfer to bulk exciton states. Furthermore, the yield of charge separation is low.
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Ramraj, Anitha. "Computational modelling of intermolecular interactions in bio, organic and nano molecules." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/computational-modelling-of-intermolecular-interactions-in-bio-organic-and-nano-molecules(7a41f3cd-1847-4ccf-8853-5fd8be2a2c15).html.
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We have investigated the noncovalent interactions in carbohydrate-aromatic interactions which are pivotal to the recognition of carbohydrates in proteins. We have employed quantum mechanical methods to study carbohydrate-aromatic complexes. Due to the importance of dispersion contribution to the interaction energy, we mainly use density functional theory augmented with an empirical correction for the dispersion interactions (DFT-D). We have validated this method with a limited number of high level ab initio calculations. We have also analysed the vibrational and NMR chemical shift characteristics using the DFT-D method. We have mainly studied the complexes involving β-glucose with 3-methylindole and p-hydroxytoluene, which are analogues of tryptophan and tyrosine, respectively. We find that the contribution for interaction energy mainly comes from CH/π and OH/π interactions. We find that the interaction energy of complexes involving CH/π and OH/π interactions is reflected in the associated blue and red shifts of vibrational spectrum. We also find that the interactions involving 3-methylindole are somewhat greater than those for p-hydroxytoluene. The C-H blueshifts are also in parallel with the predicted NMR proton shift. We have also tested different density functionals including both standard density functionals and newly developed M0x functionals and MP2 method for studying carbohydrate-aromatic complexes. The DFT-D method and M06 functionals of the M0x family are found to perform better, while B3LYP and BLYP functionals perform poorly. We find that the inclusion of a dispersion term to BLYP is found to perform better. The dispersion energy dominates over the interaction energy of carbohydrate-aromatic complexes. From the DFT-D calculations, we found that the complexes would be unstable without the contribution from dispersive energy. We have also studied the importance of noncovalent interactions in functionalization of nanotubes by nucleic acid bases and aromatic amino acids by using semi-empirical methods with dispersion term such asPM3-D and PM3-D*. We find that the both semi-empirical schemes give reasonable interaction energies with respect to DFT-D interaction energies. We have also used PM3-D method to study the adsorption of organic pollutants on graphene sheet and on nanotubes. We found that the semi-empirical schemes, which are faster and cheaper, are suitable to study these larger molecules involving noncovalent interactions and can be used as an alternative to DFT-D method. We have also studied the importance of dispersion interaction and the effect of steric hindrance in aggregation of functionalized anthracenes and pentacenes. We have also employed molecular dynamics simulation methods to study the aggregation of anthracene molecules in toluene solution.
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Roseveare, Thomas Michael. "Utilising intermolecular interactions to propagate and sustain a series of porous materials." Thesis, University of Sheffield, 2018. http://etheses.whiterose.ac.uk/19907/.
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Mullaney, John Connor. "Weak intermolecular interactions of imidazole, urea and thiourea studied by microwave spectroscopy." Thesis, University of Newcastle upon Tyne, 2017. http://hdl.handle.net/10443/4022.
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Microwave spectroscopy is a powerful spectroscopic tool in determining the structure of gas phase molecules. The microwave spectra of imidazole, urea or thiourea containing complexes such as (C3N2H4)2, (H2N)2CO...HNCO, (H2N)2CO...C3H4N2, and H2O...CS(NH2)2 have been recorded. The spectrum of various isotopologues have been measured in order to determine structural information. The geometry of these weakly bound complexes is investigated, alongside the nature of the weak intermolecular interactions present. A chirped-pulse Fourier transform microwave spectrometer (CP-FTMW) has been used in the work detailed in this thesis to measure the spectra of such molecules. The instrument allows measurement of spectra over the full range of 6.5-18.5 GHz. The molecules presented in this thesis were formed as a result of laser vaporisation of solid organic precursors in the presence of argon introduced from a pulsed nozzle. The subsequent supersonic expansion generates rotationally cool molecules (~2 K) and stabilises the weakly bound complexes. The (C3N2H4)2 complex was found to adopt a twisted configuration with a single stabilising intermolecular hydrogen bond. The (H2N)2CO...HNCO complex was observed to adopt an almost planar structure, forming two intermolecular hydrogen bonds. The N-H group of HNCO acts as both a hydrogen bond donor and acceptor. The (H2N)2CO...C3H4N2 complex was found to adopt a conformation where two intermolecular hydrogen bonding interactions around the N-H group of imidazole are present. Finally the H2O...CS(NH2)2 complex was found to contain two intermolecular hydrogen bonds, where water acts as a donor and acceptor forming S...H and O...H interactions. The results of ab initio calculations at the DFT (density functional theory), MP2 (second order Møller-Plesset perturbation theory) and CC (coupled cluster) level of theory are presented and compared to experimental results.
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Si, Chao. "Theoretical Study of Intermolecular Interactions in Protein-Drug Binding and Protein Folding." University of Toledo / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1341632548.
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Grumbling, Emily Rose. "Electronic Structure, Intermolecular Interactions and Electron Emission Dynamics via Anion Photoelectron Imaging." Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/195933.
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This dissertation explores the use of anion photoelectron imaging to interrogate electronic dynamics in small chemical systems with an emphasis on photoelectron angular distributions. Experimental ion generation, mass selection, laser photodetachment and photoelectron imaging were performed in a negative-ion photoelectron imaging spectrometer described in detail. Results for photodetachment from the simplest anion, H⁻, are used to illustrate fundamental principles of quantum mechanics and provide basic insight into the physics behind photoelectron imaging from a pedagogical perspective. This perspective is expanded by introducing imaging results for additional, representative atomic and small molecular anions (O⁻, NH₂⁻ and N₃⁻) obtained at multiple photon energies to address the energy-dependence of photoelectron angular distributions both conceptually and semi-quantitatively in terms of interfering partial photoelectron waves. The effect of solvation on several of these species (H⁻, O⁻, and NH₂⁻) is addressed in photoelectron imaging of several series of cluster anions. The 532 and 355 nm energy spectra for H⁻(NH₃)n and NH₂⁻(NH₃)n (n = 0-5) reveal that these species are accurately described as the core anion solute stabilized electrostatically by n loosely coordinated NH3 molecules. The photoelectron angular distributions for solvated H⁻ deviate strongly from those predicted for unsolvated H⁻ as the electron kinetic energy approaches zero, indicating a shift in the partial-wave balance consistent with both solvation-induced perturbation (and symmetry-breaking) of the H⁻ parent orbital and photoelectron-solvent scattering. The photoelectron energy spectra obtained for the cluster series [O(N₂O)n]⁻ and [NO(N₂O)n]⁻ indicate the presence of multiple structural isomers of the anion cores, the former displaying sharp core-switching at n = 4, the latter isomer coexistence over the entire range studied. The photoelectron angular distributions for detachment from the O⁻(N₂O)n and NO⁻(N₂O)n isomers deviate strongly from those expected for bare O⁻ and NO⁻, respectively, in the region of an anionic shape resonance of N₂O, suggesting resonant photoelectron-solvent scattering. Partial-wave models for two-centered photoelectron interference in photodetachment from dissociating I₂⁻ is presented and discussed in the context of previous results. New time-resolved photoelectron imaging results for I₂⁻, for both parallel and perpendicular pump and probe beam polarizations, are presented and briefly discussed. Finally, new ideas and directions are proposed.
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RENDINE, STEFANO. "MODELLING INTERMOLECULAR FORCES IN BIOMOLECULES: FROM PROTEIN-PROTEIN INTERACTIONS TO HALOGEN BONDS." Doctoral thesis, Università degli Studi di Milano, 2012. http://hdl.handle.net/2434/167913.
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The accurate description and evaluation of the intermolecular interactions has a great importance in the molecular modelling of biological systems.
Protein-protein interactions, in particular, being involved in virtually every cellular process, are nowadays the object of thorough studies aimed at the understanding and modulation of the underlying mechanism. In the Part I of the present work, it will be shown how, through a computational approach, it is possible to get an in-depth analysis of the network of interactions occurring at the interface between tubulin subunits and how vinblastine, a commonly used anticancer agents, is able to interfere with the correct protein association, so having a therapeutic effect. In the Part II, the self-association of the bacterial protein FtsZ will be studied, showing that the detailed description of the protein-protein interactions can provide key information for the de-novo design of inhibiting molecules.
Finally, in the Part II, the attention will be focused on the computational study of halogen bonding, which is found to have a great relevance in the recognition process between biological macromolecules and halogenated agents. In particular, it will be shown that a specific approach is mandatory for its correct description in the framework of the classical force-fields.
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Hedin, Linnea E. "Intra- and intermolecular interactions in proteins : Studies of marginally hydrophobic transmembrane alpha-helices and protein-protein interactions." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-42856.
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Most of the processes in a living cell are carried out by proteins. Depending on the needs of the cell, different proteins will interact and form the molecular machines demanded for the moment. A subset of proteins called integral membrane proteins are responsible for the interchange of matter and information across the biological membrane, the lipid bilayer enveloping and defining the cell. Most of these proteins are co-translationally integrated into the membrane by the Sec translocation machinery. This thesis addresses two questions that have emerged during the last decade. The first concerns membrane proteins: a number of α-helices have been observed to span the membrane in the obtained three-dimensional structures even though these helices are predicted not to be hydrophobic enough to be recognized by the translocon for integration. We show for a number of these marginally hydrophobic protein segments that they indeed do not insert well outside of their native context, but that their local sequence context can improve the level of integration mediated by the translocon. We also find that many of these helices are overlapped by more hydrophobic segments. We propose, supported by experimental results, that the latter are initially integrated into the membrane, followed by post-translational structural rearrangements. Finally, we investigate whether the integration of the marginally hydrophobic TMHs of the lactose permease of Escherichia coli is facilitated by the formation of hairpin structures. However our combined efforts of computational simulations and experimental investigations find no evidence for this. The second question addressed in this thesis is that of the interpretation of the large datasets on which proteins that interact with each other in a cell. We have analyzed the results from several large-scale investigations concerning protein interactions in yeast and draw conclusions regarding the biases, strengths and weaknesses of these datasets and the methods used to obtain them.At the time of the doctoral defense the following publications were not published and had a status as follows: Paper 2: In press; Paper 4 Manuscript.
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Jiemchooroj, Auayporn. "First-principles calculations of long-range intermolecular dispersion forces." Licentiate thesis, Linköping : Dept. of Electrical Engineering, Linköping University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-7512.
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Benedek, Nicole Ann, and n. benedek@gmail com. "Interactions in ionic molecular crystals." RMIT University. Applied Sciences, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20070109.161440.
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We have used ab initio computational simulation techniques to investigate both intra- and intermolecular interactions in a novel family of ionic organophosphonate molecular crystals. We have examined the influence of various numerical approximations on the computed geometry and binding energies of a selection of well-characterised hydrogen bonded systems. It was found that numerical basis sets provided the efficiency required to study the large hydrogen bonded dimer anions present in the organophosphonate system, while also producing accurate geometries and binding energies. We then calculated the relaxed structures and binding energies of phenylphosphonic acid dimer in the two arrangements in which it is present in the bulk crystal. The computed geometries were in excellent agreement with the experimental structures and the binding energies were consistent with those found for other ionic hydrogen bonded systems. Electron density maps were used to gain insight into the nature of the hydrogen bonding interaction between phenylphosphonic acid dimers. We also examined the effect of aromatic ring substituents on the geometry and energetics of the hydrogen bonding interaction. The nitro-substituted dimer was predicted to have a stronger binding energy than its unsubstituted parent while the methyl-substituted dimer was predicted to have a similar binding energy to its unsubstituted parent. An analysis of crystal field effects showed that the structure of the phenylphosphonic acid dimers in the organophosphonates is a complex product of competing intra- and intermolecular forces and crystal field effects. Cooperative effects in the organophosphonate system were also investigated and it was found that the interactions were mostly one-body (local) in nature. We have examined the intramolecular charge-transfer interaction between copper-halogen cations in the organophosphonate materials. The origin of geometric differences between the Cu(I) starting material and Cu(II) product cations was attributed to the electronic configuration of the Cu ion, not crystal field effects. To gain further insight into the difference in electronic structure between the starting material and product, we attempted to simulate the step-by-step dissociation of the [CuI]+ system. Although this investigation was not successful, we were able to expose some of the pitfalls of simulating dissociating odd-electron systems. We also analysed and compared the charge-transfer interaction in the chloro-, bromo- and iodo-forms of the organophosphonate family. The charge-transfer interaction was predicted to increase on going from the chloro- to the iodo-form, consistent with solid-state UV-visible data. Finally, we used the highly accurate Quantum Monte Carlo (QMC) method to investigate the hydrogen bonding interaction in water dimer and to calculate the dissociation energy. The accuracy of the experimental estimate for the dissociation energy has recently been questioned and an alternative value has been put forward. Our results lend support to the validity of the alternative value and are also in excellent agreement with those from other high-level calculations. Our results also indicate that QMC techniques are a promising alternative to traditional wavefunction techniques in situations where both high accuracy and efficiency are important.
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Broder, Charlotte Kate. "Diffraction studies of hydrogen bonding and other intermolecular interactions in organic crystal structures." Thesis, Durham University, 2002. http://etheses.dur.ac.uk/3886/.
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In this work three different approaches to the study of intermolecular interactions are shown. The aim is to further the understanding of specific intermolecular interactions with a view to eventually allowing the prediction and design of crystal structures from the initial molecular building blocks: crystal engineering. All three approaches make use of crystal structural information derived from X-ray and/or neutron diffraction studies. The three approaches are: • Data base approach. Specifically, the study of occurrence of hi- and tri-furcated hydrogen bonds in the Crystallographic Structural Database, and the analysis of the frequency with which they occur and the geometric restrictions of such interactions.• Analysis of a series of compounds, where there are small changes in the molecular structure as the series progresses. The influence of these changes in the molecular structure on the crystal structure is considered. The series studied was the 4-amino- 4'-hydroxydiphenylalkanes as well as some of the corresponding 4-amino-4'- hydroxydiphenylsulphides and -alkylsulphides.• Detailed analysis of individual structures to identify the intermolecular interactions that are influencing the structure. The compounds analysed in this part were 2,4,6- m.s-(4-chlorophenoxy)-l,3,5-triazene co-crystallised with tribromobenzene, triphenylisocyanurate co-crystallised with trinitrobenzene, 4,4'-dinitrotetrapheny 1 methane, 2,3-dichloro-l,4-diethynyl-l,4-dihydroxy-napthalene and, 4,4-diphenyl- 2,5-cyclohexadienone.
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Haji, Masri Mohammad K. Z. "The effect of intermolecular interactions and disorder on exciton diffusion in organic semiconductors." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/6928.
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This thesis presents studies of exciton diffusion in organic semiconductors measured using exciton-exciton annihilation and the measurements were performed on materials important for organic solar cells. In the conjugated polymer poly(3-hexylthiophene) (P3HT), the effect of molecular weight (4-76 kgmol⁻¹) was explored. Using exciton-exciton annihilation measurements, the highest diffusion coefficient was observed in the intermediate molecular weight region and was correlated with long conjugation lengths, higher fraction of aggregated states and more delocalised excitons within the aggregate. The results demonstrated that the molecular weight dependence is due to a complex relationship between intermolecular interactions, aggregate size and Boltzmann statistics. This thesis also includes an investigation of exciton diffusion in diketopyrrolopyrrole(DPP)-based small molecules as a function of molecular structure. Significant changes in photophysical and exciton diffusion properties were observed due to minor changes in molecular structure. Long conjugation lengths, bulky side chains or reduced steric hindrance due to absence of end alkyl chains correlated with reduced film crystallinity and reduced diffusion coefficients. The increase in disorder observed due to large conformational torsions resulted in inhomogeneous broadening of density of states and as a result exciton diffusion becomes dispersive. In this case, a slowdown of exciton diffusion is observed. This study demonstrates that enhanced exciton diffusion can be achieved by designing more rigid and planar conjugated backbones with smaller conjugation lengths. Finally, exciton diffusion measurements were used to rationalise the performance of T3 truxene oligomers as explosive sensors. Side chain lengths were found to have a subtle influence on exciton diffusion. Time-resolved PL quenching measurements were used to estimate the quencher concentration. Differences in quencher concentration were observed suggesting different interaction strengths of the quencher with the truxene oligomer which help explain the explosive sensing performance.
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Doherty, Ciaran Patrick Anthony. "Pulling apart the intermolecular interactions of the Parkinson's disease linked protein alpha synuclein." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/19116/.
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Amyloidoses are a group of protein misfolding diseases that are characterised by the abnormal accumulation of highly ordered filamentous assemblies known as amyloid. This phenomenon is associated with more than 50 human diseases, some of which are the most debilitating disorders that threaten human health today. Many of these disorders have age as the main contributing risk factor and, therefore, pose an ever-increasing risk in the developed world with aging societies. Despite intense research, much remains unknown about the fundamental processes driving protein aggregation in these diseases and there are few disease modifying treatments available. A protein that undergoes amyloid formation and causes disease is the intrinsically disordered neuronal protein α-synuclein (αSyn), the aggregation of which leads to several diseases including Parkinson’s disease (PD) which is the second-most common neurodegenerative disorder that affects 2–3% of the population ≥65 years of age. Importantly, the toxic species on the aggregation pathway are difficult to identify and determine in molecular detail. This thesis was motivated by this fact and aimed to study the initial intermolecular events in αSyn self-assembly (dimerisation) on a single molecule scale. Single molecule force spectroscopy (SMFS) methodologies were therefore utilised in order to study these early protein-protein interaction events. A display system was firstly designed and validated in which small regions of highly aggregation-prone sequences can be presented in a protein scaffold in a robust and reproducible manner for SMFS studies. It was demonstrated that intermolecular interactions of these sequences could be analysed by implementing this system. A novel heterodimeric interaction between the central aggregation-prone regions of αSyn (residues 71-82) and the same region of its human homologue γSynuclein (γSyn), were revealed by using this system. Further study led to the finding that this interaction played a role in the inhibiting the aggregation of αSyn. The dimerisation interaction of full length αSyn has also been analysed in this thesis and several important findings have been demonstrated. The SMFS experiments show that force-resistant structure forms in the dimeric species of αSyn and that this structure is dependent on the environmental conditions. SMFS utilising different immobilisation regimes of αSyn have also allowed the location of a novel interaction interface involving the N-terminal region of the protein. Further SMFS experiments investigating the effects of salt and hydrophobicity have on dimerisation, alongside bioinformatics analyses of the protein sequence led to the hypotheses that the dimeric interaction is driven by hydrophobic stretches in the N-terminal region, but modulated by local electrostatics. In vitro aggregation assays and SMFS on non-aggregation-prone synuclein homologues (β- and γSyn) indicated that that this interaction is protective against aggregation, considering these finding with existing literature prompted speculation that the interactions observed in SMFS may indeed be physiologically relevant. This may therefore be an important finding in regards to targeting the aggregation process with disease modifying agents.
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Takakado, Akira. "Studies on Reaction Dynamics and Interdomain/Intermolecular Interactions of LOV Light-sensor Proteins." Kyoto University, 2018. http://hdl.handle.net/2433/232272.
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McKee, Matthew Gary. "The Influence of Branching and Intermolecular Interactions on the Formation of Electrospun Fibers." Diss., Virginia Tech, 2005. http://hdl.handle.net/10919/29370.
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The implications of chain topology and intermolecular interactions on the electrospinning process were investigated for linear and randomly branched polymers. Empirical correlations were developed based on solution rheological measurements that predict the onset of electrospun fiber formation and average fiber diameter. In particular, for neutral, non-associating polymer solutions, the minimum concentration required for fiber formation was the entanglement concentration (Ce), and uniform, bead-free fibers were formed at 2 to 2.5 Ce. This was attributed to entanglement couplings stabilizing the electrospinning jet and preventing the Raleigh instability. Moreover, the influence of molar mass and degree of branching on electrospun fiber diameter was eliminated when the polymer concentration was normalized with Ce, and the fiber diameter universally scaled with C/Ce to the 2.7 power.
Polymers modified with quadruple hydrogen bonding groups were investigated to determine the role of intermolecular interactions on the solution rheological behavior and the electrospinning process. In nonpolar solvents, the hydrogen bonding functionalized polymers displayed significant deviation from the electrospinning behavior for neutral solutions due to the strong intermolecular associations of the multiple hydrogen bonding groups. The predicted electrospinning behavior was recovered when the hydrogen bonding interactions were screened with a polar solvent. Moreover, it was observed that branching and multiple hydrogen bonding afforded significant processing advantages compared to functionalized, linear analogs of equal molar mass. For example, branched chains in the unassociated state possessed a larger Ce compared to the linear chains, which indicated a lower entanglement density of the former. However, in the associated state the linear and branched chains possessed nearly equivalent Ce values, suggesting a similar entanglement density. Thus, the branched polymers displayed significantly lower viscosities in the unassociated state compared to linear polymers, while still retaining sufficient entanglements in the associated state due to the reversible network structure of the multiple hydrogen bond sites.
The solution rheological and processing behavior of polyelectrolyte solutions was also investigated to discern the role of electrostatic interactions on electrospun fiber formation. In particular, the polyelectrolyte solutions formed nano-scale electrospun fibers with an average fiber diameter 2 to 3 orders of magnitude smaller than neutral polymer solutions of equivalent viscosity and C/Ce. This was attributed to the very high electrical conductivity of the polyelectrolyte solutions, which imparted a high degree of charge repulsion in the electrospinning jet and increased the extent of plastic stretching in the polymer filament. In fact, the average diameter of the polyelectrolyte fibers under certain conditions was less than 100 nm, which makes them good candidates for protective clothing applications due to their high specific surface area. Moreover, the neutral polymer solution electrospinning behavior was recovered after the addition of NaCl, which screened the electrostatic charge repulsions along the polyelectrolyte main chain. Finally, electrospun, biocompatible phospholipid membranes were produced from solutions of entangled worm-like lecithin micelles. This is the first example of successfully electrospinning low molar mass, amphiphilic compounds into uniform fibers. Electrospinning the phospholipid worm-like micelles into nonwoven fibrous mats will afford direct engineering of bio-functional, high surface area membranes without the use of multiple synthetic steps, complicated electrospinning setups, or post processing surface treatments.Ph. D.
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Fabianski, Robert. "Modeling of intermolecular interactions and stability in molecular crystals : experiments and computer simulations." Montpellier 2, 2001. http://www.theses.fr/2001MON20223.
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