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Dissertations / Theses on the topic '030606 Structural Chemistry and Spectroscopy'

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Published: 10 December 2022
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1

Sinnamon, Brendan Francis. "Application of FT-IR spectroscopy to the study of Langmuir and Langmuir-Blodgett films of vinyl octadecanoate." Thesis, University of Queensland, 1996.

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2

Momot, Konstantin I. "Studies of Nuclear Magnetic Relaxation Processes in Paramagnetic Metalloporphyrin Complexes." Thesis, University of Arizona, 1998. https://eprints.qut.edu.au/127462/1/Momot_PhDthesis_1998.pdf.

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Temperature dependence of Nuclear Magnetic Resonance (NMR) chemical shifts and longitudinal and transverse relaxation times (T1 and T2) was studied for the pyrrole protons in a number of six-coordinate S=1/2 iron(III) tetraphenylporphyrin (TPP) and tetramesitylporphyrin (TMP) complexes in the temperature range 190---310 K. In all complexes, temperature behavior of the chemical shifts and relaxation times is consistent with the presence of a low spin - high spin exchange caused by the dissociation of one axial ligand. In symmetric sterically hindered complexes, cyclic exchange induced by the synchronous rotation of axial ligands is also present. In all complexes, T2s are considerably shorter than T1s. Relaxation times in the TMP complexes are generally longer than corresponding values for the TPP complexes. Estimate of the electronic T1 is given and mechanisms of nuclear relaxation are discussed. The rate of NOE buildup for a pair of pyrrole protons in [TMPFe(2-MeImH)2]+ was measured; it is consistent with the Stokes rotational correlation time. A method is proposed to predict the detectability and optimum detection conditions of NOE between a pair of structurally rigid protons in similar complexes. Contrary to previous studies, no NOE is detected between pyrrole protons of two unsymmetrically substituted bis-N-methylimidazole Fe(III) TPP complexes. Two NMR approaches were utilized to measure the rate constant of axial ligand rotation in the TMP complex. Saturation transfer measurements yield overestimated rate constant. The measurement based on the temperature dependence of the T2s (ΔH‡ = 48 ± 1 kJ/mol, ΔS‡ = -10 ± 6 J/K  mol) is consistent with previous studies. Modified MM2 potentials were also used to study the rotation of axial ligands in [TMPFe(1,2-Me2Im)2]+ and [TPPFe(1-MeIm)2]+. Adiabatic potential energy surfaces (PES) for rotation of axial ligands were constructed for both complexes. Synchronous rotation of the axial ligands (ΔH‡ = 48 kJ/mol) is highly preferable in the TMP complex. For the TPP complex, the enthalpy barriers to synchronous and asynchronous rotation are 3.3 and 5.4 kJ/mol, respectively. The relationship between the orientation of axial ligands, distortion of metallo¬porphy¬rin core from planarity, and the bulkiness of axial ligands and porphyrin substituents is discussed.
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3

Conrad, Andrew Ryan. "Rotational Spectroscopy of Biomolecules." Kent State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=kent1309478136.

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4

Rhodes, C. J. "Structural studies of organic and organosilicon free radicals by ESR spectroscopy." Thesis, University of Sussex, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.370439.

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5

Sangha, Satindra P. "Kinetic, equilibrium and structural studies on imidodithiodiphosphinates and hydroxyoximes." Thesis, University of Warwick, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340963.

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6

Li, Yan 1978. "Structural studies of carbon storage regulator, CsrA, from Escherichia coli by NMR spectroscopy." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=81358.

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CsrA of E. coli is a global regulatory RNA binding protein with a putative KH domain. My thesis work has been focused on characterization of the CsrA protein and its interactions with RNA by NMR spectroscopy. Gel filtration and PFG-NMR diffusion experiments indicate that CsrA primarily exists in oligomerized form, while acidic pH favors the formation of a dimer. The NMR structural characterization was carried out with the dimer form of CsrA. The CsrA subunit consists of five anti-parallel beta-sheets and one alpha-helix with a flexible C-terminus. The dimer is formed by sharing beta-sheets. Interactions of CsrA with RNA have been monitored by NMR. Upon titration with a 15-mer RNA (CACACGGAUUGUGUG), a complex was formed in slow exchange on the NMR timescale and gave rise to a large conformational change in the CsrA structure. The three-dimensional structure and the binding titration provide new insights into the regulatory mechanism.
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7

Gucinski, Ashley Christine. "Gas Phase Structural Studies of Peptide Fragment Ions: Structural Insights into Mass Spectrometry Fragmentation Mechanisms." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/202766.

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This dissertation presents extensive structural studies of gas-phase peptide fragment ions, with a specific focus on b₂⁺ ions. Fragment ion structures can provide important insights into peptide fragmentation mechanisms. Based on the structures formed, information about the preference of competing b ion formation pathways can be obtained. b₂⁺ ion structures are of interest because of their large relative abundances in MS/MS spectra, which are difficult to predict. Prior to this work, only a few b₂⁺ ion structures were determined; these systems featured only aliphatic residues and all formed oxazolones. The work presented herein examines the influence of basic, acidic, and backbone-attached sidechains on peptide fragmentation mechanisms, as revealed by the resulting b₂⁺ fragment ion structure(s) formed. Specifically, the structures of several histidine, aspartic acid, and proline-containing b₂⁺ ions are determined by using action IRMPD spectroscopy, fragment ion HDX, and DFT calculations. The structures of a series of histidine analogue-containing b₂⁺ ions reveal that the location and availability of the pi-nitrogen is essential for diketopiperazine formation. The histidine sidechain bulk or strain interferes with the complete trans-cis isomerization required for diketopiperazine formation, so the oxazolone structure is also present. Xxx- Pro b₂⁺ ions favor oxazolone formation with aliphatic N-terminal residues. HP favors the diketopiperazine, combining the histidine effect and the proline cis conformation propensity. For Xxx-Asp b₂⁺ ions, aspartic acid significantly influences b₂⁺ ion structure only with an N-terminal histidine or lysine; both HD and KD form a mixture of oxazolone, anhydride, and diketopiperazine structures, presenting the first spectroscopic evidence for the anhydride b₂⁺ion structure. The HA and AH b₂⁺ ions feature the same structures, but HP and PH do not, showing that residue position matters. Additionally, while relative intensities and HDX rates featured some fluctuation, peptide precursor composition differences did not alter the mixture of b₂⁺ ion structures formed for a given b₂⁺ ion. To complement existing gas-phase structural methods, the utility of a new technique, QCID-HDX-IRMPD, was applied to m/z 552.28 from YAGFL-OH. Both the standard b₅⁺ fragment ion and an isobaric non-C-terminal water loss ion are present. Without separation of these isomers, MS/MS spectral interpretation would be complicated.
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8

Perera, Rehani Shinuka. "Determining the Structural Dynamics and Topology of Canonical HOLIN-S05 Using EPR Spectroscopy." Miami University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=miami1591797430542798.

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9

Maciejewski, Mark William. "Structural characterization of compact peptides from staphylococcal nuclease by circular dichroism and nuclear magnetic resonance spectroscopy /." The Ohio State University, 1996. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487936356160363.

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10

Gao, Min. "Structural and Dynamic Studies of Supramolecular Assemblies by Solid State NMR Spectroscopy." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385135235.

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11

Perry, Richard John. "Structural studies on high oxidation state nickel complexes and their nickel(II) precursors using EXAFS spectroscopy." Thesis, University of Southampton, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358484.

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12

Nordmark, Eva-Lisa. "Structural and Interaction Studies of Bacterial Polysaccharides by NMR Spectroscopy." Doctoral thesis, Stockholm : Institutionen för organisk kemi, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-284.

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13

Shannon, Matthew D. "High Resolution Structural and Dynamic Studies of Biomacromolecular Assemblies using Solid-State NMR Spectroscopy." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1534321838601796.

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14

Bottorf, Lauren Marie. "Developing Electron Paramagnetic Resonance Spectroscopy Methods for Secondary Structural Characterization of Membrane Proteins." Miami University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=miami1510164534760125.

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15

Ghebreysus, Woldu Mengistu. "Quantum mechanical and experimental infra-red studies on stability and structural properties of substituted acylthiourea compounds." Thesis, Stellenbosch : Stellenbosch University, 2004. http://hdl.handle.net/10019.1/50073.

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16

Morris, Daniel Lamon. "Solvent/solute interactions probed by picosecond transient Raman spectroscopy : study of S(1) 1,4-diphenyl-1,3-butadiene and its structural analogues /." The Ohio State University, 1995. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487864485230264.

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17

Nadaud, Philippe S. "High-Resolution Structural Studies of Paramagnetic Proteins by Multidimensional Solid-State Nuclear Magnetic Resonance Spectroscopy." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1268318234.

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18

King, Albert W. "Structural Characterization and Spectroscopic Investigation of Isomerization Dynamics inPhotochromic Polypyridyl Ruthenium(II) Chelating mono- and bis-Sulfoxide Complexes." Ohio University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1427716619.

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19

Malizia, Jason Patrick. "Structural, Spectroscopic, and Kinetic Investigation of Modified Photochromic Ruthenium Sulfoxide Complexes." Ohio University Honors Tutorial College / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1398971012.

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20

Nusair, Nisreen A. "Investigating the Structural and Dynamic Properties of Spin-Labeled Fatty Acids and Proteins Incorporated into Magnetically Aligned Bicelles Utilizing EPR Spectroscopy." Miami University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=miami1123180888.

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21

Regoutz, Anna. "Structural and electronic properties of metal oxides." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6f425890-b211-4b35-b438-b8de18f7ae64.

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Metal oxides are of immense technological importance. Their wide variety of structural and electronic characteristics leads to a flexibility unrivalled by other groups of materials. However, there is still much debate about the fundamental properties of some of the most widely used oxides, including TiO2 and In2O3. This work presents high quality, in-depth characterisation of these two oxides in pure and doped form, including soft and hard X-ray photoelectron spectroscopy and X-ray diffraction. Bulk samples as well as thin film samples were prepared analysed. For the preparation of thin films a high quality sol-gel dip-coating method was developed, which resulted in epitaxial films. In more detail the organisation of the thesis is as follows: Chapter 1 provides an introduction to key ideas related to metal oxides and presents the metal oxides investigated in this thesis, In2O3, Ga2O3, Tl2O3, TiO2, and SnO2. Chapter 2 presents background information and Chapter 3 gives the practical details of the experimental techniques employed. Chapters 4 presents reciprocal space maps of MBE-grown In2O3 thin films and nanorods on YSZ substrates. Chapters 5 and 6 investigate the doping of In2O3 bulk samples with gallium and thallium and introduce a range of solid state characterisation techniques. Chapter 7 describes the development of a dip-coating sol-gel method for the growth of thin films of TiO2 and shows 3D reciprocal space maps of the resulting films. Chapter 8 concerns hard x-ray photoelectron spectroscopy of undoped and Sn-doped TiO2. Chapter 9 interconnects previous chapters by presenting 2D reciprocal space maps of nano structured epitaxial samples of In2O3 grown by the newly developed sol-gel based method. Chapter 10 concludes this thesis with a summary of the results.
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22

Stone, Shane Ramsay. "Structural characterisation of the solution and membrane-associated conformations of human little gastrin and its bioactive fragments by NMR spectroscopy and molecular modelling." Doctoral thesis, University of Cape Town, 2006. http://hdl.handle.net/11427/6289.

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The solution studies aimed to determine the conformations of a series of DMSO solubilised gastrin peptides, G-4, [ß-Ala ¹] G-5 and G-17, so as to establish how the configurations of the biologically relevant sequence were related to each other, and to resolve whether they adopted preferred and conserved conformations in solution. Interproton distance restraints were calculated from measured NOe crosspeak intensities for each peptide.
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23

Gul, Sheraz. "Synthesis, Optical and Structural Characterization, and Exciton Dynamics of Doped ZnSe Nanocrystals, and, Simultaneous X-ray Emission Spectroscopy of Two Elements Using Energy Dispersive Spectrometer." Thesis, University of California, Santa Cruz, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3630692.

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Doped semiconductor quantum dots (QDs) comprise an important subclass of nanomaterials in which a small quantity of impurity is added intentionally, adding another degree of freedom to alter their size-dependent physical and electronic properties. Intense, tunable, long lived and stable photoluminescence make them quintessential candidates for many opto-electronic applications including solid-state lighting, display devices and biomedical imaging. ZnSe QDs, which are blue-emitting fluorophores, were doped with Cu+1 to redshift their photoluminescence (PL) to green region of the visible spectrum. These Cu-doped ZnSe QDs were then codoped with Al3+, Ga 3+ and In3+ to improve the PL quantum yield (QY) by eliminating the defect states originating from charge imbalance created by aliovalent doping. Codoping also resulted in further redshifting of the PL, covering most of the visible spectrum, making them potential candidates for use in solid-state lighting and as optical down converters in next generation light emitting diodes (LEDs). To better understand the optical properties of these materials, local structure around the luminescent centers was investigated by extended X-ray absorption fine structure (EXAFS). Cu was found to occupy a distorted tetrahedral site with the codopant residing in a substitutional Zn site. Based on the structural information obtained by EXAFS, density functional theory calculations (DFT) were performed to get a clear picture of the energy levels associated with the electronic transitions. Furthermore, the dynamics studies of the exciton and charge carriers were carried out to get deeper insight of the various photophysical processes involved. The fluorescence lifetime was increased approximately 10 times after doping.

The multielectron catalytic reactions often involve multimetallic clusters, where the reaction is controlled by the electronic and spin coupling between metals and ligands to facilitate charge transfer, bond formation/breaking, substrate binding, and release of products. A method was developed to detect X-ray emission signal from multiple elements simultaneously to probe the electronic structure and sequential chemistry that occurs between the elements. A wavelength dispersive spectrometer based on the von-Hamos geometry was used, that disperses Kβ emission signals of multiple elements onto an area detector, and enables an XES spectrum to be measured in a single-shot mode. This overcomes the scanning needs of the Rowland circle spectrometers, and the data is free from temporal and normalization errors, and therefore ideal to follow sequential chemistry at multiple sites. This method was applied to MnOx based electrocatalysts, and the effect of Ni addition was investigated. Electro-deposited Mn oxide catalyses oxygen-evolution reaction (OER) and oxygen-reduction reaction (ORR) at different electrochemical potentials under alkaline condition. Incorporation of Ni reduced the low valent Mn component resulting in higher average oxidation state of Mn in MnNiOx under ORR and OER conditions, when compared to MnO x under similar conditions. The reversibility of the electrocatalyst was also found to improve by the inclusion of Ni.

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24

Conroy, Daniel William. "Structural Studies of Biomolecules by Dynamic Nuclear Polarization Solid-State NMR Spectroscopy." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1555428362333615.

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25

Premadasa, Uvinduni I. "Insights into the Role of Structural Modification on the Surface Molecular Interactions Probed Using Sum Frequency Generation Spectroscopy." Ohio University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1578394424376667.

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26

Ahammad, Tanbir. "Probing the structural dynamics, conformational change, and topology of pinholin S21, a bacteriophage lytic protein, using electron paramagnetic resonance spectroscopy." Miami University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=miami1595598100557068.

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27

Yu, Xueting. "Probing Small Molecules and Membrane Protein Structures Utilizing Solid-state NMR Spectroscopy." Miami University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=miami1343059572.

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28

Olsson, Ulrika. "Structural Studies of O-antigen polysaccharides, Synthesis of 13C-labelled Oligosaccharides and Conformational Analysis thereof, using NMR Spectroscopy." Doctoral thesis, Stockholm University, Department of Organic Chemistry, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7283.

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In order to understand biological processes, to treat and diagnose diseases, find appropriate vaccines and to prevent the outbreak of epidemics, it is essential to obtain more knowledge about carbohydrate structures. This thesis deals with structure and conformation of carbohydrates, analysed by NMR spectroscopy and MD simulations.In the first two papers, the structures of O-antigen polysaccharides (PS) from two different E. coli bacteria were determined using NMR spectroscopy. The O-antigenic PS from E. coli O152 (paper I) consists of branched pentasaccharide repeating units, built up of three different carbohydrate residues and a phosphodiester, whilst the repeating unit of the O-antigen from E. coli O176 (paper II) is built up of a linear tetrasaccharide consisting of two different monosaccharides.

In papers III and IV, the conformational analysis of different disaccharides is described. Conformational analysis was performed using NMR spectroscopy and MD simulations (paper IV). In paper III four different glucobiosides were studied using coupling constants and Karplus-type relationships. By use of specific 13C isotopically labelled derivatives, additional coupling constants were obtained and the number of possible torsion angles was reduced by half. In paper IV, we examine the conformations of two disaccharides that are part of an epitope of malignant cells. From NOE and T-ROE experiments, short proton-proton distances around the glycosidic linkage were estimated. Furthermore, interpretation of the extracted coupling constants using Kaplus relationships gave the values of the torsion angles. As in paper III, isotopically labelled compounds were synthesised in order to enhance the sensitivity of the analysis. Finally, MD simulations were performed and the results were compared with results from NMR data.

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29

Nickels, Elizabeth Anne. "Structural and thermogravimetric studies of group I and II borohydrides." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:f18f8f7c-1837-4b96-b4bb-5f964e93899c.

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This thesis investigates the structure and thermal behaviour of LiBH4, NaBH4, KBH4, LiK(BH4)2, Ca(BH4)2 and Sr(BH4)2. LiK(BH4)2 is the first mixed alkali metal borohydride and was synthesised and characterised during this work. The crystal structures of these borohydrides were studied using variable temperature neutron and synchrotron X-ray diffraction. The synthesis of isotopically enriched samples of 7Li11BD4, Li11BD4, Na11BD4 and K11BD4 allowed high quality neutron diffraction data to be collected. Particular attention was paid to the exact geometry of the borohydride ions which were generally found to be perfect tetrahedra but with orientational disorder. New structures of Ca(BH4)2 were identified and the first crystal structure of Sr(BH4)2 was determined from synchrotron X-ray diffraction data. Solid state 11B NMR and Raman spectroscopy provided further information about the structure of these borohydrides. The thermal behaviour of the borohydrides was investigated using thermogravimetric analysis with mass spectrometry of the decomposition gas products. Hydrogen is the main decomposition gas product from all of these compounds but small amounts of B2H6 and BH3 were also detected during decomposition. Thermogravimetic analyses of Na11BD4 and K11BD4 were completed whilst collecting in-situ neutron diffraction data allowing information about structural changes and mass losses to be combined in order to better understand the decomposition process.
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30

Feldmann, Erik A. "Biophysical characterization of heterocyst differentiation regulators, HetR and PatS, from the cyanobacterium, Anabaena sp. strain PCC 7120 and structural biology of bacterial proteins from the Northeast Structural Genomics Consortium." Miami University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=miami1342801532.

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31

Anthis, Nicholas J. "Structural studies of integrin activation." Thesis, University of Oxford, 2009. http://ora.ox.ac.uk/objects/uuid:caf0f76f-b05a-4b72-8394-5f24de3fd5df.

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Fundamental to cell adhesion and migration, integrins are large heterodimeric membrane proteins that link the extracellular matrix to the actin cytoskeleton. Uniquely, these adhesion receptors mediate inside-out signal transduction, whereby extracellular adhesion is activated from within the cell by talin, a large cytoskeletal protein that binds to the cytoplasmic tail of the β integrin subunit via its PTB-like F3 domain. Features of the interface between talin1 and small β3 fragments only have been described previously. Through NMR studies of full-length integrin β tails, we have found that β tails differ widely in their interactions with different talin isoforms. The muscle-specific β1D/talin2 complex exhibited particularly high affinity, leading to the X-ray crystal structure of the β1D tail/talin2 F2-F3 complex. Further NMR and biological experiments demonstrated that integrin activation is induced by a concerted series of interactions between the talin F3 domain and the β tail and between the talin F2 domain and the cell membrane. Additional studies revealed the structural determinants of tight talin2/β1D binding and the basis of more general differences between β1 and β3 talin binding. NMR studies were also performed on tyrosine-phosphorylated integrin tails binding to the PTB domains of talin1 and Dok1, an inhibitor of integrin activation; these revealed that phosphorylation can inhibit integrin activation by increasing the affinity of the β tail for talin competitors. Key residues governing this switch were identified, and proteins were engineered with reversed affinities, offering potentially useful biological tools. Taken together, these results reveal the remarkable complexity of structural features that enable talin and its competitors to mediate this important form of transmembrane signalling.
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32

Asare, Shardrack O. "Optimized Acid/Base Extraction and Structural Characterization of β-glucan from Saccharomyces Cerevisiae." Digital Commons @ East Tennessee State University, 2015. https://dc.etsu.edu/etd/2513.

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β-glucan is a major component of the fungal cell wall consisting of (1→3)-β linked glucose polymers with (1→6)-β linked side chains. The published classical isolation procedure of β-glucan from Saccharomyces cerevisiae is expensive and time-consuming. Thus, the aim of this research was to develop an effective procedure for the extraction of glucans. We have developed a new method for glucan extraction that will be cost effective and will maintain the native structure of the glucan. The method that we developed is 80% faster and utilizes 1/3 of the reagents compared to the published classical method. Further, the method developed increases the yield from 2.9 % to 10.3 %. Our new process has a branching frequency of 18.4 down from 197 and a side chain of 5.1 up from 2.5. The data indicate a more preserved native structure of isolated glucans.
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33

Cottee, Matthew A. "Building the Drosophila centriole : a structural investigation of the centriolar Proteins SAS-6, SAS-4 and Ana2." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:b43c6848-56bd-4806-ba34-ed2cde59b294.

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The centriole is a complex cylindrical assembly found in the cells of ciliated eukaryotes. It serves two important roles in the cell: templating the growth of cilia, and forming the basis of the centrosome, which is the major microtubule organising centre in the cell. Cilia and centrosomes are involved in many cellular processes, from signalling to cell division and differentiation. As such, defects in centriole assembly can have downstream consequences on these processes and are linked to a variety of human diseases including cancer and microcephaly. The complex superstructure of the centriole has fascinated biologists for decades. It comprises a nine-fold, radially symmetric array of microtubule triplet blades attached to a central cartwheel structure. During the last two decades, proteomic analyses have identified many proteins that are associated with the centriole. However, genetic studies have shown that only a surprisingly small number of these proteins are essential for the biogenesis of the centriole. In Drosophila melanogaster, three such essential proteins, SAS-6, Ana2 and SAS-4 are required in the early stages of centriole biogenesis. In this thesis I have investigated the assembly steps involving these key players from a structural perspective. I have identified and recombinantly expressed functional domains of these proteins in order to characterise them in vitro. Using X-ray crystallography and other biophysical techniques, I have been able to define mechanisms for several steps involved in the assembly of these proteins. In collaboration with colleagues in the laboratory I have been able to investigate the biological significance of these essential assembly steps in vivo. This information has provided novel insights into the molecular, and even atomic, detail of the initial steps of centriole assembly, including an explanation of a natural point mutation involved in human microcephaly.
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34

Poplaukhin, Pavel V. "Ytterbium(II) - group 6, 7 transition metal carbonyl complexes systematic synthesis and structural characterization /." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1154373668.

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35

Brackett, Claudia Lindblom. "NMR characterization of a diiron macrocycle and structural characterization of a diketo derivative." Scholarly Commons, 2001. https://scholarlycommons.pacific.edu/uop_etds/554.

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The time-dependent visible spectra and the crystal structure of [Fe2(C20H24N8O2)(CH3CN)4]·PF6 (diketo-dimer) were studied. The spectra showed that the most significant chemistry occurred during the initial 1.5 hours of the synthetic reaction. The starting materials 343 nm peak shifted to a lower energy, at 360 nm, and a new shoulder appeared at 490 nm. This change suggests the formation of a new intermediate whose spectrum has an exceptional resemblance to the starting materials mixed valent species, [Fe2(TIED)(Cl)4]+1 (TIED = tetraiminethylene dimacrocycles). Two isosbestic points were found at 538 and 371 nm. The diketo-dimer's crystals appear to have individual colors, a physical characteristic called pleochroism. Pleochroism is a topic in the study of optical crystallography which is discussed and applied to the diketo-dimer. The extinction angle was estimated to be 14°, a value consistent for triclinic crystals. X-ray crystallography found that the diketo-dimer is triclinic, and has a space group of P-1. A noteworthy feature is the bond length, 1.406 Å, between the two linking bridgehead carbons. This bond length matches the value for partial double bonds of aromatic compounds. This argues for a delocalized electron circulating within the macrocycle. The NMR spectra of a diiron macrocycle, [Fe2(TIED)(CH3CN)4]4+, were examined. Temperature dependent, pH dependent, D+ substitution, selectively decoupled, and COSY 1H NMR experiments were performed. Two sets of structural equilibria were found. One set is temperature dependent, and the other is pH dependent. Of particular interest are the peaks centered at 9.7 ppm and assigned to the imine carbon protons H2. Its resonance indicates an imine proton in an extensively conjugated aromatic environment with an electron deficient metal.
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36

Dunn, James A. "From organometallic cations to carbenes : an NMR, structural and reactivity study /." *McMaster only, 1998.

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37

Lundborg, Magnus. "Computer-Assisted Carbohydrate Structural Studies and Drug Discovery." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-56411.

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Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-antigen polysaccharides are presented, both a structure determination by NMR and also research on glycosyltransferases which assemble the polysaccharides. The computer program CASPER has been improved to assist in carbohydrate studies and in the long run make it possible to automatically determine structures based only on NMR data. Detailed computer studies of glycans can shed light on their interactions with proteins and help find inhibitors to prevent unwanted binding. The WaaG glycosyltransferase is important for the formation of E. coli lipopolysaccharides. Molecular docking analyses of structures confirmed to bind this enzyme have provided information on how inhibitors could be composed. Noroviruses cause gastroenteritis, such as the winter vomiting disease, after binding human histo-blood group antigens. In one of the projects, fragment-based docking, followed by molecular dynamics simulations and binding free energy calculations, was used to find competitive binders to the P domain of the capsid of the norovirus VA387. These novel structures have high affinity and are a very good starting point for developing drugs against noroviruses. The protein targets in these two projects are carbohydrate binding, but the techniques are general and can be applied to other research projects.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.
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38

Sehgal, Rippa. "Binding of Oxaliplatin and its Analogs with DNA Nucleotides at Variable pH and Concentration Levels." TopSCHOLAR®, 2016. http://digitalcommons.wku.edu/theses/1602.

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Oxaliplatin is one of the three FDA-approved platinum anticancer drugs and considered a third generation drug, discovered after the first generation drug cisplatin and second generation drug carboplatin. It is known to react with proteins and DNA nucleotides in the body. Reaction with DNA occurs primarily at guanosine residues and secondarily at adenine residues for oxaliplatin and other platinum drugs. We have previously studied oxaliplatin and an analog with additional steric hindrance in the amine ligand and found that the analog had different reactivity with methionine. Now, we have prepared oxaliplatin and its three analogs Pt(Me2dach)(ox), Pt(en)(ox) and Pt(Me4en)(ox) and have reacted each platinum compound with both guanine and adenine nucleotides at pH 4 and pH 7 at different molar ratios. These reactions have been characterized by Nuclear Magnetic Resonance (NMR) spectroscopy equipment over time to observe the formation of products and compare them on the basis of their kinetics and binding affinities. NMR has shown that even under the conditions of excess platinum, the dominant products are usually those with two nucleotides coordinated to one platinum center. Reactions are faster at pH 7 than pH 4 due to deprotonation of phosphate group. Reactions of GMP with a platinum center are faster than reaction with AMP because of the chelate formed by the oxalate ligand. The extra methyl groups on the oxaliplatin analogs do not appear to slow down the reactions with nucleotides considerably. The pH generally affects the rate but does not substantially affect the product distribution.
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39

Alomar, Taghrid Saad. "Directing the assembly of multicomponent organic crystals : synthesis, characterisation and structural analysis of multicomponent organic systems formed from dynamic processes." Thesis, University of Bradford, 2014. http://hdl.handle.net/10454/7163.

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Directed assembly of molecular solids continues to attract widespread interest with its fundamental application in a wide range of commercial settings where control of the crystalline state of materials corresponds with product performance. These arenas include pharmaceuticals, personal care formulations, foods, paints and pigments and explosives. In recent times, the assembly of multicomponent organic systems has achieved considerable impetus with the widespread interest in co-crystal systems. However, cogent assembly (or engineering) of multicomponent materials is still in its infancy. Considerable advances in crystal design have been made through consideration of intermolecular ‘synthons’ – identifiable motifs utilising hydrogen bonds – but the translation of other molecular information (conformation, chirality, etc.) into solid state properties (e.g. long-range (translational) symmetry, crystal chirality) remains poorly understood. In this study, we have attempted to evaluate the influence of a chiral centre adjacent to molecular synthons to identify potential translation of information into the solid form. We have compared the co-crystallisation of nicotinamide with both the racemic mixture of malic acid against that with an enantiomerically pure form of the acid (L-malic acid). As well as DL-phenyllactic acid and L-phenyllactic acid. iii It is apparent that recognition between enantiomeric molecular forms play a significant role in the assembly of these systems. This mechanism can be considered independently from the H-bonding networks supporting the hetero-molecular interactions (e.g. acid-amide recognition). Discrimination and control of such interactions may play a role in transmitting chiral molecular information into solid state multi-component assemblies. In order to develop an understanding of co-crystal formation in chiral and achiral forms with intermolecular interactions, the CSD and crystal structures were obtained to do the analysis of how co-crystals pack. This study has also investigated the use of boronic acids. The aim of this study was to investigate the modification of the hydrogen bonding environment within the hydrogen bonded multi-component systems of boroxines. The study also attempted to determine how the starting materials drive the systems between the boronic acid co-crystal and the boroxine adduct.
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40

Alomar, Taghrid S. "Directing the Assembly of Multicomponent Organic Crystals. Synthesis, characterisation and structural analysis of multicomponent organic systems formed from dynamic processes." Thesis, University of Bradford, 2014. http://hdl.handle.net/10454/7163.

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Abstract:
Directed assembly of molecular solids continues to attract widespread interest with its fundamental application in a wide range of commercial settings where control of the crystalline state of materials corresponds with product performance. These arenas include pharmaceuticals, personal care formulations, foods, paints and pigments and explosives. In recent times, the assembly of multicomponent organic systems has achieved considerable impetus with the widespread interest in co-crystal systems. However, cogent assembly (or engineering) of multicomponent materials is still in its infancy. Considerable advances in crystal design have been made through consideration of intermolecular ‘synthons’ – identifiable motifs utilising hydrogen bonds – but the translation of other molecular information (conformation, chirality, etc.) into solid state properties (e.g. long-range (translational) symmetry, crystal chirality) remains poorly understood. In this study, we have attempted to evaluate the influence of a chiral centre adjacent to molecular synthons to identify potential translation of information into the solid form. We have compared the co-crystallisation of nicotinamide with both the racemic mixture of malic acid against that with an enantiomerically pure form of the acid (L-malic acid). As well as DL-phenyllactic acid and L-phenyllactic acid. iii It is apparent that recognition between enantiomeric molecular forms play a significant role in the assembly of these systems. This mechanism can be considered independently from the H-bonding networks supporting the hetero-molecular interactions (e.g. acid-amide recognition). Discrimination and control of such interactions may play a role in transmitting chiral molecular information into solid state multi-component assemblies. In order to develop an understanding of co-crystal formation in chiral and achiral forms with intermolecular interactions, the CSD and crystal structures were obtained to do the analysis of how co-crystals pack. This study has also investigated the use of boronic acids. The aim of this study was to investigate the modification of the hydrogen bonding environment within the hydrogen bonded multi-component systems of boroxines. The study also attempted to determine how the starting materials drive the systems between the boronic acid co-crystal and the boroxine adduct.
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41

Sahakyan, Aleksandr B. "Extending the boundaries of the usage of NMR chemical shifts in deciphering biomolecular structure and dynamics." Thesis, University of Cambridge, 2012. https://www.repository.cam.ac.uk/handle/1810/243642.

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NMR chemical shifts have an extremely high information content on the behaviour of macromolecules, owing to their non-trivial dependence on myriads of structural and environmental factors. Although such complex dependence creates an initial barrier for their use for the characterisation of the structures of protein and nucleic acids, recent developments in prediction methodologies and their successful implementation in resolving the structures of these molecules have clearly demonstrated that such barrier can be crossed. Furthermore, the significance of chemical shifts as useful observables in their own right has been substantially increased since the development of the NMR techniques to study low populated 'excited' states of biomolecules. This work is aimed at increasing our understanding of the multiple factors that affect chemical shifts in proteins and nucleic acids, and at developing high-quality chemical shift predictors for atom types that so far have largely escaped the attention in chemical shift restrained molecular dynamics simulations. A general approach is developed to optimise the models for structure-based chemical shift prediction, which is then used to construct CH3Shift and ArShift chemical shift predictors for the nuclei of protein side-chain methyl and aromatic moieties. These results have the potential of making a significant impact in structural biology, in particular when taking into account the advent of recent techniques for specific isotope labelling of protein side-chain atoms, which make large biomolecules accessible to NMR techniques. Through their incorporation as restraints in molecular dynamics simulations, the chemical shifts predicted by the approach described in this work create the opportunity of studying the structure and dynamics of proteins in a wide range of native and non-native states in order to characterise the mechanisms underlying the function and dysfunction of these molecules.
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42

Whitaker, Darren A. "Method Development for the Application of Vibrational Spectroscopy to Complex Organic-Inorganic Materials in Astrobiology. A Systematic Development of Raman Spectroscopy and Related Analytical Methods to the Structural Chemistry at Organic (Biological) and Inorganic (Mineralogical) Interfaces of Material Assemblies Relevant to Astrobiology and Inter-Planetary Science." Thesis, University of Bradford, 2013. http://hdl.handle.net/10454/7332.

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In the search for the conformation of extant or extinct life in an extraterrestrial setting the detection of organic molecular species which may be considered diagnostic of life is a key objective. These molecular targets comprise a range of distinct chemical species, with recognisable spectroscopic features. This project aims to use these features to develop an in-situ molecular specific Raman spectroscopic methodology which can provide structural information about the organic–inorganic interface. The development of this methodology identified a surface enhanced Raman spectroscopic technique, that required minimal sample preparation, allowed for the detection of selected organic species immobilised on an inorganic matrix and was effective for quantities below those which conventional dispersive Raman spectroscopy would detect. For the first time spectral information was gained which allowed analysis of the organic–inorganic interface to be carried out, this gave an insight into the orientation with which molecules arrange on the surfaces of the matrices. Additionally a method for the detection of organic residues intercalated into the interlamellar space of smectite type clays was developed. An evaluation of the effectiveness of uni and multivariate methods for the analysis of large datasets containing a small number of organic features was also carried out, with a view to develop an unsupervised methodology capable of performing with minimal user interaction. It has been shown that a novel use of the Hotellings T2 test when applied to the principal component analysis of the datasets combined with SERS allows identification of a small number of organic features in an otherwise inorganic dominated dataset. Both the SERS and PCA methods hold relevance for the detection of organic residues within interplanetary exploration but may also be applied to terrestrial environmental chemistry.
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43

Millard, Christopher John. "Structural and functional characterisation of the collagen binding domain of fibronectin." Thesis, University of Oxford, 2007. http://ora.ox.ac.uk/objects/uuid:af0ec9b5-8789-498e-a1b7-5887ca1ad03f.

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Fibronectin is an extracellular multidomain glycoprotein that directs and regulates a variety of cell processes such as proliferation, development, haemostasis, embryogenesis, and wound healing. As a major component of blood, fibronectin exists as a soluble disulphide linked dimer, but it can also be incorporated into an insoluble cross-linked fibrillar network to form a major component of the extracellular matrix. Fibronectin is composed of an extended chain of module repeats termed Fn1, Fn2, and Fn3 that bind to a wide range of transmembrane receptors and extracellular matrix components, including collagen. The gelatin binding domain of fibronectin was first isolated as a 45kDa proteolytic fragment and has since been found to be composed of six modules: 6Fn1-1Fn2-2Fn2-7Fn1-8Fn1-9Fn1 (in this notation nFX represents the nth type X module in the native protein). This domain has been reported to bind to both collagen and denatured collagen (gelatin), but with 10-100 times higher affinity to the latter; it can be purified to homogeneity on a gelatin affinity column. In the work presented here, fragments of the gelatin binding domain are expressed in P. pastoris, purified to homogeneity, and investigated at the molecular level. Through a dissection approach, surface plasmon resonance (SPR) is used to characterise the recombinantly produced protein, to accumulate more information about the function of the full domain. NMR is used to assess the folding of the protein fragments at atomic resolution. In particular, the secondary structure of 8Fn1-9Fn1 is mapped using inter-strand NOEs, which suggests that the construct takes the fold of a pair of typical Fn1 modules. Gelatin affinity chromatography is used to confirm that both Fn1 and Fn2 modules contribute to gelatin binding, possibly in two clusters (1Fn2-2Fn2 and 8Fn1-9Fn1). The 7Fn1 module may perform a structural role in linking together these two interaction sites, in the same way as suggested for 6Fn1, which is thought to act in a structural manner to enhance the binding of 1Fn2-2Fn2 to gelatin. Three carbohydrate moieties are found on this domain, one on 2Fn2 and two on 8Fn1. Here, by means of expressing different protein length fragments, and by site directed mutagenesis, the role of each sugar chain is investigated independently. The sugar chain on 2Fn2 does not appear to promote binding to collagen, nor does the first sugar chain on 8Fn1 (N-linked to N497), implying another role for these sugars such as protection from proteolysis. However, the presence of at least a single GlcNAc sugar residue on the second sugar chain site on 8Fn1 (N- linked to N511) is essential for full affinity binding to collagen. Direct binding of the 8Fn1-9Fn1 module pair to collagen is assessed with a short collagen peptide and the binding is monitored by NMR. The peptide appears to bind, predominantly to the final strand of 8Fn1, the first β- strand of 9Fn1, and the linker between the two modules, with μM affinity. A model for bound peptide is proposed. The highly conserved amino acid motif Ile-Gly-Asp (IGD) is found on four of the nine N-terminal Fn1 modules of fibronectin. Tetrapeptides containing the IGD were demonstrated to promote the migration of fibroblast cells into a native collagen matrix. Two of these “bioactive” IGD motifs are found within the gelatin binding domain, one on 7Fn1 and one on 9Fn1. In this study, the motif in the 8Fn1-9Fn1 module pair is shown to be located in a tightly constrained loop within 9Fn1. By site directed mutagenesis, the IGD motifs of 7Fn1 and 9Fn1 are subjected to single amino acid substitutions, and their ability to stimulate cell migration assessed in our assay. By NMR, the fold of the IGD mutant proteins is found to be unaffected by the mutation with respect to the wild type, with the exception of small perturbations around the substitution site. While the wild type module is able to stimulate fibroblast migration, the mutant proteins show reduced or negligible bioactivity. The larger fragments show far more potency in stimulating fibroblast migration, with 8Fn1-9Fn1 (one IGD motif) 104 times more potent than the IGD peptide, and the full gelatin binding domain (two IGD motifs) 106 times more potent than the 8Fn1-9Fn1. Potential mechanisms for this enormous enhancement of the IGD potency in different contexts are discussed.
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44

Whitaker, Darren Andrew. "Method development for the application of vibrational spectroscopy to complex organic-inorganic materials in astrobiology : a systematic development of Raman spectroscopy and related analytical methods to the structural chemistry at organic (biological) and inorganic (mineralogical) interfaces of material assemblies relevant to astrobiology and inter-planetary science." Thesis, University of Bradford, 2013. http://hdl.handle.net/10454/7332.

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Abstract:
In the search for the conformation of extant or extinct life in an extraterrestrial setting the detection of organic molecular species which may be considered diagnostic of life is a key objective. These molecular targets comprise a range of distinct chemical species, with recognisable spectroscopic features. This project aims to use these features to develop an in-situ molecular specific Raman spectroscopic methodology which can provide structural information about the organic–inorganic interface. The development of this methodology identified a surface enhanced Raman spectroscopic technique, that required minimal sample preparation, allowed for the detection of selected organic species immobilised on an inorganic matrix and was effective for quantities below those which conventional dispersive Raman spectroscopy would detect. For the first time spectral information was gained which allowed analysis of the organic–inorganic interface to be carried out, this gave an insight into the orientation with which molecules arrange on the surfaces of the matrices. Additionally a method for the detection of organic residues intercalated into the interlamellar space of smectite type clays was developed. An evaluation of the effectiveness of uni and multivariate methods for the analysis of large datasets containing a small number of organic features was also carried out, with a view to develop an unsupervised methodology capable of performing with minimal user interaction. It has been shown that a novel use of the Hotellings T2 test when applied to the principal component analysis of the datasets combined with SERS allows identification of a small number of organic features in an otherwise inorganic dominated dataset. Both the SERS and PCA methods hold relevance for the detection of organic residues within interplanetary exploration but may also be applied to terrestrial environmental chemistry.
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45

Kelly, Michael Jon. "Hybrid ferrocene-based systems." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:fd46594d-98d6-4f8a-a6ab-eb5ee74ba7f3.

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This thesis explores the capacity of sterically and electronically unsaturated boranes to bind substrates of biological and environmental interest, and transduce such binding events into a photo-physical and/or electrochemical response, hence reporting the presence of these substrates. Chapter three details the synthesis of a range of novel ferrocenyl boranes featuring either a proximal hydrogen-bond donor or a second Lewis acidic centre. These novel boranes were shown to be competent at binding both cyanide and fluoride anions, with the role played by a proximal hydrogen-bond donor or a second Lewis acidic centre in anion binding investigated by both NMR and crystallographic studies. Chapter four reports the synthesis of novel pyridinyl and related boronic esters, as well as unexpected mixed alkenyl/aryl boranes. The capacity of both types of system to bind fluoride or cyanide anions in solution was investigated by UV-Vis and NMR studies. The photo-physical responses to these anions were also probed, leading to the establishment of both switch-on and switch-off fluorescent responses. Chapter five extends the knowledge derived from selective anion receptor design and combines this with recent developments in the field of frustrated Lewis pairs (FLPs) to activate, bind and report the presence of nitrous oxide (N2O) molecule. Thus, the syntheses of novel, highly Lewis acidic ferrocenyl boranes that incorporate a high degree of steric loading around the boron centre are reported. The electrochemical and photo-physical response of an FLP system to the presence of N2O was investigated leading to the development of a novel N2O reporting system.
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46

Solcan, Nicolae Claudiu. "Biochemical and biophysical studies of the prokaryotic proton dependent oligopeptide transporters." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:5ad900fb-a949-4bac-b69a-f585b44a8382.

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The proton dependent oligopeptide transporters (POT family) are members of the Major Facilitator Superfamily of secondary active transporter proteins. They use the transmembrane proton gradient to drive the uptake of di- and tripeptides into the cytoplasm. Members of the family are highly conserved in pro- and eukaryotic genomes, and in humans they are responsible for the oral absorption of many drug families, including -lactam antibiotics. Recently, the crystal structures of PepTSo and PepTSt, two prokaryotic homologues of the human proteins PepT1 and PepT2, captured the proteins in two distinct conformations, providing insight into the structural aspects of the transport mechanism. A protocol was designed for functional liposome reconstitution of POT proteins, and transport assays were conducted to characterise their substrate specificity, pH dependence and kinetic properties. Using site-directed mutagenesis, we identified binding site residues involved in peptide recognition and proton translocation, and distinguished between the two roles by comparing protein activity in proton- and peptide-driven conditions. We also investigated the roles of key residues in the conformational transitions that accompany the transport cycle, using data from biochemical assays, molecular dynamics simulations and modeling, as well as electron paramagnetic resonance measurements. In addition, several bacterial POT members were screened for crystallisation, in order to assess their stability and crystal diffraction quality in different detergents. Further work was performed with bacterial POT homologues YdgR and GkPOT, including binding studies using NMR spectroscopy and assaying drug transport in vivo and in vitro. Together, the data establish bacterial POTs as model systems for studying the mammalian oligopeptide transporters, and a mechanistic model for peptide transport is proposed.
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47

Slater, Craig Stephen. "Studies of photoinduced molecular dynamics using a fast imaging sensor." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:24b6edce-9bd0-4729-97d6-4de959618cb0.

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Few experimental techniques have found such a diverse range of applications as has ion imaging. The field of chemical dynamics is constantly advancing, and new applications of ion imaging are being realised with increasing frequency. This thesis is concerned with the application of a fast pixelated imaging sensor, the Pixel Imaging Mass Spectrometry (PImMS) camera, to ion imaging applications. The experimental possibilities of such a marriage are exceptionally broad in scope, and this thesis is concerned with the development of a selection of velocity-map imaging applications within the field of photoinduced molecular dynamics. The capabilities of the PImMS camera in three-dimensional and slice imaging applications are investigated, in which the product fragment Newton-sphere is temporally stretched along the time-of-flight axis, and time-resolved slices through the product fragment distribution are acquired. Through experimental results following the photodissociation of ethyl iodide (CH3CH2I) at around 230 nm, the PImMS camera is demonstrated to be capable of recording well-resolved time slices through the product fragment Newton-sphere in a single experiment, without the requirement to time-gate the acquisition. The various multi-hit capabilities of the device represent a unique and significant advantage over alternative technologies. The details of a new experiment that allows the simultaneous imaging of both photoelectrons and photoions on a single detector for each experimental acquisition cycle using pulsed ion extraction are presented. It is demonstrated that it is possible to maintain a high velocity resolution using this approach through the simultaneous imaging of the photoelectrons and photoions that result from the (3 + 2) resonantly enhanced multi-photon ionisation of Br atoms produced following the photodissociation of Br2 at 446.41 nm. Pulsed ion extraction represents a substantial simplification in experimental design over conventional photoelectron-photoion coincidence (PEPICO) imaging spectrometers and is an important step towards performing coincidence experiments using a conventional ion imaging apparatus coupled with a fast imaging detector. The performance of the PImMS camera in this application is investigated, and a new method for the determination of the photofragment detection efficiencies based on a statistical fitting of the coincident photoelectron and photoion data is presented. The PImMS camera is applied to laser-induced Coulomb explosion imaging (CEI) of an axially chiral substituted biphenyl molecule. The multi-hit capabilities of the device allow the concurrent detection of individual 2D momentum images of all ionic fragments resulting from the Coulomb explosion of multiple molecules in each acquisition cycle. Correlations between the recoil directions of the fragment ions are determined through a covariance analysis. In combination with the ability to align the molecules in space prior to the Coulomb explosion event, the experimental results demonstrate that it is possible to extract extensive information pertaining to the parent molecular structure and fragmentation dynamics following strong field ionisation. Preliminary simulations of the Coulomb explosion dynamics suggest that such an approach may hold promise for determining elements of molecular structure on a femtosecond timescale, bringing the concept of the `molecular movie' closer to realisation. Finally, the PImMS camera is applied to the imaging of laser-induced torsional motion of axially chiral biphenyl molecules through femtosecond Coulomb explosion imaging. The target molecules are initially aligned in space using a nanosecond laser pulse, and torsional motion induced using a femtosecond 'kick' pulse. Instantaneous measurements of the dihedral angle of the molecules are inferred from the correlated F+ and Br+ ion trajectories following photoinitiated Coulomb explosion at various time delays after the initial kick pulse. The technique is extended to include a second kick pulse, in order to achieve either an increase in the amplitude of the oscillations or to damp the motion, representing a substantial degree of control of the system. Measurements out to long kick-probe delays (200 ps) reveal that the initially prepared torsional wave packet periodically dephases and rephases, in accordance with the predictions of recent theoretical work.
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48

Irwin, Mark Robert Floyd. "The synthesis and characterisation of metal complexes containing chemically reduced bipyridyl ligand systems." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:44dd8d43-01cf-4a2a-ab66-c7cab1d9201f.

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This thesis describes the synthesis and characterisation of metal complexes that contain chemically reduced bipyridyl ligands. The crystal structures of twenty-six novel complexes are reported alongside detailed discussions on the electronic and spectroscopic effects and trends associated with the different oxidation states within these species. Chapter One introduces the isomers of bipyridine and their redox chemistry, the concept of non-innocent ligands and the spectroscopic techniques that are currently used in determining ligand oxidation states. Subsequently, examples of main group, transition metal, lanthanide and actinide species that contain or may contain reduced forms of the ligand are discussed. Chapter Two details the synthesis and structural characterisation of alkali metal salts of singly and doubly reduced forms of the three commercially available bipyridine isomers. The effects of this reduction are investigated with the aim of developing diagnostic fingerprints for each of the ligand oxidation states. Chapter Three discusses the synthesis of an homologous series of compounds of the form [M(2,2'-bipy)(mes)2]n– where M = Cr, Mn, Fe, Co, Ni and n = 0, 1. Trends in magnetism, bonding and electronic structure are investigated with reference to theoretical calculations and the diagnostic fingerprints identified in the previous chapter. Chapter Four describes the synthesis and characterisation of three compounds containing the isostructural motif [Zn2(4,4'-bipy)(mes)4]n– where n = 0, 1, 2. Structural and spectroscopic changes are discussed and com- pared to theoretical calculations. Chapter Five contains descriptions of the spectroscopic techniques employed in the above research and synthesis routes to all compounds featured in this thesis.
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49

Unsal, Emre. "Integrated Real Time Studies to Track all Physical and Chemical Changes in Polyimide Film Processing From Casting to Imidization." University of Akron / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=akron1384129535.

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50

Millan, Cabrera Reisel. "Computational study of heterogeneous catalytic systems. Kinetic and structural insights from Density Functional Theory." Doctoral thesis, Universitat Politècnica de València, 2021. http://hdl.handle.net/10251/161934.

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Abstract:
[ES] En este trabajo estudiamos dos reacciones catalíticas relevantes para la industria y la localización del anión fluoruro en la zeolita RTH, sintetizada en medio fluoruro. El capítulo 3 es el primer capítulo de resultados, donde se estudia la reducción quimioselectiva del nitroestireno en las superficies Ni(111), Co(111), Cu(111) y Pd(111). El mecanismo generalmente aceptado de esta reacción está basado en el esquema propuesto por Haber en 1898, en el que la reacción puede transcurrir por dos rutas, la directa y la de condensación. En este capítulo exploramos ambas rutas, y observamos que la ruptura de los enlaces N-O y la consecuente formación de enlaces metal-O está más favorecida que la formación de enlaces N-H en las superficies Ni(111) y Co(111), debido al carácter oxofílico de ambos metales. Las etapas más lentas involucran la formación de enlaces N-H. En las superficies de metales nobles como Pt(111) y Pd(111) se observa el comportamiento contrario. La superficie Cu(111) es un caso intermedio comparado con los metales nobles y no nobles. Además, el nitroestireno interactúa con los átomos de Cu de la superficie solo a través de grupo nitro, con lo cual es un candidato ideal para alcanzar selectividades cerca del 100%. Sin embargo, la superficie Cu(111) no es capaz de activar la molécula de H2. En este sentido, proponemos un catalizador bimetálico basado en Cu, dopado con otro metal capaz de activar al H2, tales como el Pd o el Ni. En los capítulos 4 y 5 se ha estudiado la reducción catalítica selectiva de los óxidos de nitrógeno (SCR, en inglés) con amoníaco. Usando métodos de DFT, hemos encontrado rutas para la oxidación de NO a NO2, nitritos y nitratos con energías de activación relativamente bajas. También, hemos encontrado que la reducción de Cu2+ a Cu+ requiere la participación simultánea de NO y NH3. Posteriormente, hemos estudiado la influencia del NH3 en este sistema con métodos de dinámica molecular. El NH3 interacciona fuertemente con el Cu+ de forma que dos moléculas de este gas son suficientes para romper la coordinación del catión Cu+ con los oxígenos del anillo 6r, y formar el complejo lineal [Cu(NH3)2]+. Además, los cationes Cu2+ pueden ser estabilizados fuera de la red mediante la formación del complejo tetraamincobre(II). Debido a la presencia de los cationes Cu+ y Cu2+ coordinados a la red de la zeolita, aparecen bandas en la región entre 800-1000 cm-1 del espectro infrarrojo. El análisis de las frecuencias IR de varios modelos con Cu+ y Cu2+ coordinados al anillo 6r, o formando complejos con amoniaco indica que cuando los cationes Cu+ y Cu2+ están coordinados a los oxígenos del anillo 6r aparecen vibraciones entre 830 y 960 cm-1. Frecuencias en esta zona también se obtienen en los casos en que NO, NO2, O2 y combinaciones de dos de ellos están adsorbidos en Cu+ y Cu2+. Sin embargo, cuando los cationes Cu+ y Cu2+ están fuera del anillo (no hay enlaces entre los cationes de cobre y los oxígenos del anillo 6r) no se obtienen vibraciones de IR en esta región del espectro. Estos resultados indican que con el seguimiento del espectro IR durante la reacción SCR es posible determinar si los cationes Cu+ y Cu2+ están coordinados o no al anillo de 6r en las etapas de oxidación y reducción. Por último, hemos simulado el desplazamiento químico de 19F, δiso,, en la zeolita sintetizada RTH. El análisis del δiso de los distintos modelos utilizados nos ha permitido reconocer la simetría del material sintetizado, el cual pertenece al grupo espacial P1 y la nueva celda unidad ha sido confirmada experimentalmente por difracción de rayos X. Finalmente, hemos asignado la señal experimental que aparece en el espectro de 19F a -67.2_ppm, al F- localizado en un sitio T2, el cual es a su vez la posición más estable. Además, la señal a -71.8 ppm se ha asignado al anión F- localizado en un sitio T4.
[CA] En aquest treball estudiem dues reaccions catalítiques rellevants per a la indústria i la localització de l'anió fluorur en la zeolita RTH, sintetitzada al mig fluorur. El capítol 3 és el primer capítol de resultats, on s'estudia la reducció quimioselectiva del nitroestireno en les superfícies Ni(111), Co(111), Cu(111) i Pd(111). El mecanisme generalment acceptat d'aquesta reacció està basat en l'esquema proposat per Haver-hi en 1898, en el qual la reacció pot transcórrer per dues rutes, la directa i la de condensació. En aquest capítol explorem totes dues rutes, i observem que la ruptura dels enllaços N-O i la conseqüent formació d'enllaços metall-O està més afavorida que la formació d'enllaços N-H en les superfícies Ni(111) i Co(111), a causa del caràcter oxofílico de tots dos metalls. Les etapes més lentes involucren la formació d'enllaços N-H. En les superfícies de metalls nobles com Pt(111) i Pd(111) s'observa el comportament contrari. La superfície Cu(111) és un cas intermedi comparat amb els metalls nobles i no nobles. A més, el nitroestireno interactua amb els àtoms de Cu de la superfície sol a través de grup nitre, amb la qual cosa és un candidat ideal per a aconseguir selectivitats prop del 100%. No obstant això, la superfície Cu(111) no és capaç d'activar la molècula d'H2. En aquest sentit, proposem un catalitzador bimetàl·lic basat en Cu, dopat amb un altre metall capaç d'activar a l'H2, com ara el Pd o el Ni. En els capítols 4 i 5 hem estudiat la reducció catalítica selectiva dels òxids de nitrogen (SCR, en anglés) amb amoníac. Usant mètodes de DFT, hem trobat rutes per a l'oxidació de NO a NO2, nitrits i nitrats amb energies d'activació relativament baixes. També, hem trobat que la reducció de Cu2+ a Cu+ requereix la participació simultània de NO i NH3. Posteriorment, hem estudiat la influència del NH3 en aquest sistema amb mètodes de dinàmica molecular. El NH3 interacciona fortament amb el Cu+ de manera que dues molècules d'aquest gas són suficients per a trencar la coordinació del catió Cu+ amb els oxígens de l'anell 6r, i formar el complex lineal [Cu(NH3)2]+. A més, els cations Cu2+ poden ser estabilitzats fora de la xarxa mitjançant la formació del complex tetraamincobre(II). A causa de la presència dels cations Cu+ i Cu2+ coordinats a la xarxa de la zeolita, apareixen bandes a la regió entre 800-1000 cm-1 de l'espectre infraroig. L'anàlisi de les freqüències IR de diversos models amb Cu+ i Cu2+ coordinats a l'anell 6r, o formant complexos amb amoníac indica que quan els cations Cu+ i Cu2+ estan coordinats als oxígens de l'anell 6r apareixen vibracions entre 830 i 960 cm-1. Freqüències en aquesta zona també s'obtenen en els casos en què NO, NO2, O2 i combinacions de dues d'ells estan adsorbidos en Cu+ i Cu2+. No obstant això, quan els cations Cu+ i Cu2+ estan fora de l'anell (no hi ha enllaços entre els cations de coure i els oxígens de l'anell 6r) no s'obtenen vibracions d'IR en aquesta regió de l'espectre. Aquests resultats indiquen que amb el seguiment de l'espectre IR durant la reacció SCR és possible determinar si els cations Cu+ i Cu2+ estan coordinats o no a l'anell de 6r en les etapes d'oxidació i reducció. Finalment, hem simulat el desplaçament químic de 19F, δiso, en la zeolita sintetitzada RTH. L'anàlisi del δiso dels diferents models utilitzats ens ha permés reconéixer la simetria del material sintetitzat, el qual pertany al grup espacial P1 i la nova cel·la unitat ha sigut confirmada experimentalment per difracció de raigs X. Finalment, hem assignat el senyal experimental que apareix en l'espectre de 19F a -67.2 ppm, al F- localitzat en un lloc T2, el qual és al seu torn la posició més estable. A més, el senyal a -71.8 ppm s'ha assignat a l'anió F- localitzat en un lloc T4.
[EN] In this work, we have studied two heterogeneous catalytic reactions and the localization of the fluoride anion in the as-made RTH framework, synthesized in fluoride medium. The first results, included in chapter 3, correspond to the chemoselective reduction of nitrostyrene on different metal surfaces, i.e, Ni(111), Co(111), Cu(111) and Pd(111). Until very recently, the reduction of the nitro group was explained on the basis of the general mechanism proposed by Haber in 1898 where the reaction can follow two routes, the direct and condensation route. We have explored the relevant elementary steps of both routes and found that because of the oxophilic nature of Ni and Co, the steps involving the dissociation of N-O bonds and formation of metal-O bonds are significantly favored compared with the other steps on both metal surfaces. In addition, the most demanding steps in terms of energy involve the formation of N-H bonds. These findings are in contrast to those of noble metals such as Pt and Pd, where the opposite behavior is observed. The behavior of Cu(111) lies in between the aforementioned cases, and also no chemical bonds between the carbon atoms of the aromatic ring of nitrostyrene and the Cu(111) surface is formed. For this reason, it might be an ideal candidate to achieve nearly 100 % selectivity. However, the Cu(111) surface does not seem to activate the H2 molecule. In this regard, we propose a bimetallic Cu-based catalyst whose surface is doped with atoms of a H2-activating metal, such as Ni or Pd. On another matter, we have also investigated the selective catalytic reduction of nitrogen oxides (SCR-NOx) and the main results are presented in the following two chapters, 4 and 5. By using static DFT methods, we found pathways for the oxidation of NO to NO2, nitrites and nitrates with relatively low activation energies. We also found, in agreement with experimental reports, that the reduction of Cu2+ to Cu+ requires the simultaneous participation of NO and NH3. Later, molecular dynamics simulations allowed us to assess the influence of NH3. The strong interaction of NH3 with the Cu+ cation is evidenced by its ability to detach Cu+ from the zeolite framework and form the mobile linear complex [Cu(NH3)2]+. Cu+ is no longer coordinated to the zeolite framework in the presence of two NH3 molecules. This observation and the fact that the T-O-T vibrations of the framework produce bands in the 800-1000 cm-1 region of the IR spectrum when perturbed by the coordination of Cu+ and Cu2+ cations, indicate that bands in the 800-1000 cm-1 regions should be observed when both copper cations are bonded to the framework oxygens. Finally, we have also studied NMR properties of the as-made pure silica RTH framework, aiming at locating the compensating fluoride anion. The calculation of the 19F chemical shift in different T sites and comparison with the experimental NMR spectra shows that the as-made RTH belongs to the P-1 space group with 16 Si, 32 O atoms, one fluoride anion and one OSDA cation. These results have been confirmed experimentally by XRD. In addition, we have assigned the experimental signal of 19F at -67.2 ppm to the fluoride anion in a T2 site, which in turn is the most stable location found, and the signal of -71.8 ppm to a fluoride anion sitting in a T4 site.
My acknowledgements to “La Caixa foundation” for the financial support through “La Caixa−Severo Ochoa” International PhD Fellowships (call 2015), to the Spanish Supercomputing Network (RES), to the Centre de Càlcul de la Universitat de València, to the Flemish Supercomputer Center (VSC) of Ghent University for the computational resources and technical support, and to the Spanish Government through the MAT2017-82288-C2-1-P programme
Millan Cabrera, R. (2021). Computational study of heterogeneous catalytic systems. Kinetic and structural insights from Density Functional Theory [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/161934
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