Dissertations / Theses: 'Conformational studie'

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ABBIATI, GIORGIO. "Reazioni di cicloaddizione tra 1,3-diazabuta-1,3-dieni e cheteni:sintesi di diidropirimidinoni e 4-immino-azetidinoni." Doctoral thesis, Università degli Studi di Milano, 2000. http://hdl.handle.net/2434/651275.

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The work of this Ph.D. thesis is an in depth study on [4+2] and [2+2] cycloaddition reactions of 1-(4-methylphenyl) and 1-benzyl-1,3-diaza-1,3-butadienes with different ketenes, usually generated from the corresponding acid halide in the presence of a base. Reaction with phenyl, diphenyl, chloro and ethoxycarbonylketenes are described and the mechanism involved is discussed. Moreover, thermal and photochemical ring expansion reactions of azetidinones to 5,6-dihydro-3H-pyrimidin-4-ones are studied. Finally, the [2+2] cycloaddition reactions of 1-benzyl-2,4-diphenyl-1,3-diaza-1,3-butadiene with some chiral ketenes, such as beta-(dimethylphenylsilyl)ketene, beta-menthoxyketene and Evans-Sjögren ketene are investigated. The results are analysed and rationalized also on the basis of computational calculations.

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Jiao, Ding. "Conformational studies of peptides." Diss., The University of Arizona, 1992. http://hdl.handle.net/10150/186089.

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The conformational and dynamic properties of peptides play critical roles in their biological functions. Various methods have been applied for studying peptide conformations and dynamics. On the basis of structure-function studies and NMR work on the conformation of CCK, we designed a series of conformationally constrained peptides to test the hypothesis of a C-terminal folded structure required for interaction with the CCK-B receptor. Various cyclic peptides were synthesized to explore the possible spatial arrangements of key amino acid side chain groups. Based on the NMR conformational studies and receptor binding assay data, it was suggested that a C-terminal folded conformation of CCK4 is a necessary but not a sufficient structural feature for strong CCK-B receptor binding. In a series of tyrosine analogues, slow rotations around Cβ-Cγ were studied by dynamic NMR. The free energies of activation (ΔG(^≠)) at their coalescence temperatures were estimated to be in the range of 14-20 Kcal/mol. This energy barrier is comparable to the one experienced by tyrosine aromatic rings in the interior of proteins, bioactive peptides or in peptide-protein complexes. This study demonstrates the ability of conformational constraints on restricting molecular motions. These tyrosine analogues with constrained side chains can be useful tools in studying the structure-function relationships of peptides and proteins. In peptides and proteins, amino acid residues are covalently linked together by either amide bonds or disulfide bonds. The molecules Me₂S₂, N-methylacetamide and other simple amides were used as models for disulfide or peptide bond linkages in our ab initio MO studies. An angular dependence of the ¹³C and ³³S NMR chemical shifts on the C-S-S-C dihedral angle was predicted based on our calculations. The well-known syn/anti dependence of ¹³C chemical shift around the peptide bond was found to have the same origin as the angular dependence of the γ-substituent effect. A systematic geometry optimization and chemical shift calculation on a model peptide, N-acetyl-N'-methyl glycine amide, enabled us to construct the first non-empirical energy surface and ¹³C NMR chemical shift surface for this molecule. The experimentally observed correlation between ¹³C chemical shifts of Cα in amino acid residues and protein secondary structures is attributed to the effect controlled by φ and ψ dihedral angles.

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Bolin, Kimberly Anne. "Conformational studies of protein fragments." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239325.

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Norgren, Anna S. "Conformational Stability!? : Synthesis and Conformational Studies of Unnatural Backbone Modified Peptides." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7420.

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Husain, Rhonda. "Conformational studies on potentially bioactive peptides." Thesis, Queen's University Belfast, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333817.

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Smith, Timothy Andrew David. "Conformational analysis studies in NMR spectroscopy." Thesis, University of Liverpool, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243220.

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Barron, Christopher. "Conformational studies of lithium phenyl stearate." Thesis, Sheffield Hallam University, 1991. http://shura.shu.ac.uk/19323/.

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The structure and conformation of lithium phenyl stearate (and to a lesser extent, for comparative purposes, cadmium stearate) was investigated using Fourier transform infrared spectroscopy, and various modelling techniques. The infrared results for LiPS show that the aliphatic portion of the soap molecule is much more ordered at room temperature than had been expected, having only 0.62 and 0.60 gtg and gg defects per molecule respectively, where an isotropic chain would have 1.35 and 1.21 gtg and gg defects per chain respectively. As the temperature is increased the number of conformational defects increases continuously, until at < 130°C the chain reaches an isotropic degree of disorder. At this point the phase transition begins, so the chain reaches liquid like disorder before the phase transition begins. Modelling of the phenyl stearic acid showed that the phenyl group was restricted to certain angle of rotation values, and that the bonds close to the phenyl group were prevented from attaining true rotational isomeric state conformations, gtg defects near the phenyl group were distorted only slightly from their usual angular position, and an additional band in the infrared spectrum of LiPS at 1363 cm-1 has been assigned to this distorted gtg/gtg' defect. The gg defects near the phenyl group have a much greater distortion (and energy) resulting in a much reduced probability of occurrence. The number of gg defects present at the phase transition (< 130°C) was only 75% of that expected for an isotropic n-alkane of equivalent chain length, indicating that the four bonds nearest to the phenyl group have a reduced probability of forming a gg defect. The modelling of the ionic core of LiPS gives a reasonable estimate of between 5.6 to 7.1 A for the core radius. When this is used to calculate the hexagonal cylinder diameter, at room temperature, along with the average chain extension, it gives a value for the cylinder diameter of between 33.9 to 36.8A. The hexagonal lattice parameter determined by X-ray diffraction has a value 35.9A. Also after the LiPS sample has gone through the phase transition beginning at >130°C, the hexagonal lattice parameter is 31.4A while the cylinder diameter lies between 30.2 and 33.2A.Crystalline cadmium stearate was found to contain two crystal forms, orthorhombic which has lattice dimensions of a0=5.05A, b0=7.35A and c0=48.6A and the other eithermonoclinic or triclinic. In the reverse hexagonal phase, the cadmium stearate molecule behaves like an isotropic n-alkane of equivalent chain length. The model used to predict the core radius of divalent metal soaps gives rise to some inconsistencies: the cylinder diameter thus determined gives a result between 28.8A to 31.7A, while the lattice parameter determined by X-ray diffraction gives a value of 36.9A. The assumption that the n-carboxylate ions in a divalent metal soap behave like two independent monovalent metal ion soaps appears to be incorrect.

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George, Rosemary. "Synthesis and conformational studies of indolizines." Thesis, Rhodes University, 1994. http://hdl.handle.net/10962/d1005032.

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The present investigation has involved a kinetic and mechanistic study of the thermal cyclization of 3-acetoxy-3-(2-pyridyl)-2-methylenepropanoate esters and related compounds to 2-substituted indolizines. Substrates for the kinetic study were prepared via the Baylis-Hillmann reaction of pyridine-2-carboxaldehydes with acrylate esters, acrylonitrile and methyl vinyl ketone. The resulting hydroxy compounds were then acetylated to afford the acetoxy derivatives, thermal cyclization of which gave the corresponding 2-substituted indolizines. The cyclization reactions was followed using 'H NMR spectroscopy and were shown to follow firstorder kinetics. The influence of the various substituents on the observed first-order rate constants has been examined and variable temperature studies have permitted evaluation of activation parameters for the formation of methyl indolizine-2-carboxylate and ethyl indolizine-2-carboxylate. An alternative route to 2-substituted indolizines via halogenated derivatives was explored and several halogenated 2-pyridyl derivatives were synthesised and their thermal cyclization to indolizines was attempted. Novel 5-methylindolizine-2-carboxamides were prepared as part of this investigation and dynamic NMR spectroscopy was used to study internal rotation about the amide N-CO bond in these compounds.

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Ambrogi, Martina. "Synthesis, characterization and conformational studies of arylbenzylmaleimides." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2012. http://amslaurea.unibo.it/4251/.

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From the discoveries of Pasteur, stereochemistry has played an increasingly important role in the chemical sciences. In particular conformational study of molecules with axial chirality is object of intense research. Through Dynamic-NMR analysis and simulation of the spectra, the energy rotational barriers value of conformers are obtained. When this barrier is high sufficiently, atropisomeric stable compounds can be reached. They can be separated and used in stereo-synthesis and in packing processes. 3,4-bis-aryl maleimides, in which the aromatic groups are sufficiently bulky, generate atropisomeric stable configurations, that can be isolated at room temperature. The assignment of absolute configurations is performed through ECD analysis and comparison with computational calculations. The biological activities of maleimide derivatives widen the field of atropisomers application also in biological systems.

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Hallman, Kristina. "Asymmetric Catalysis : Ligand Design and Conformational Studies." Doctoral thesis, KTH, Chemistry, 2001. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3275.

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This thesis deals with the design of ligands for efficientasymmetric catalysis and studies of the conformation of theligands in the catalytically active complexes. All ligandsdeveloped contain chiral oxazoline heterocycles.

The conformations of hydroxy- and methoxy-substitutedpyridinooxazolines and bis(oxazolines) during Pd-catalysedallylic alkylations were investigated using crystallography,2D-NMR techniques and DFT calculations. A stabilising OH-Pdinteraction was discovered which might explain the differencein reactivity between the hydroxy- and methoxy-containingligands. The conformational change in the ligands due to thisinteraction may explain the different selectivities observed inthe catalytic reaction.

Polymer-bound pyridinooxazolines and bis(oxazolines) weresynthesised and employed in Pd-catalysed allylic alkylationswith results similar to those of monomeric analogues;enantioselectivities up to 95% were obtained. One polymer-boundligand could be re-used several times after removal of Pd(0).The polymer-bound bis(oxazoline) was also used in Zn-catalysedDiels-Alder reactions, but the heterogenised catalyst gavelower selectivities than a monomeric analogue.

A series of chiral dendron-containing pyridinooxazolines andbis(oxazolines) were synthesised and evaluated in Pd-catalysedallylic alkylations. The dendrons did not seem to have anyinfluence on the selectivity and little influence on the yieldwhen introduced in the pyridinooxazoline ligands. In thebis(oxazoline) series lower generation dendrimers had a postiveon the selectivity, but the selectivity and the activitydecreased with increasing generation.

Crown ether-containing ligands were investigated inpalladium-catalysed alkylations. No evidence of a possibleinteraction between the metal in the crown ether and thenucleophile was discovered.

A new type of catalyst, an oxazoline-containing palladacyclewas found to be very active in oxidations of secondary alcoholsto the corresponding aldehydes or ketones. The reactions wereperformed with air as the re-oxidant. Therefore, this is anenviromentally friendly oxidation method.

Keywords:asymmetric catalysis, chiral ligand,oxazolines, conformational study, allylic substitution,polymer-bound ligands, dendritic ligands, crown ether,oxidations, palladacycle.

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Wacowich-Sgarbi, Shirley Ann. "Synthesis and conformational studies of constrained oligosaccharides." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0013/NQ60036.pdf.

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Muir, Thomas W. "Synthesis and conformational studies of a protein." Thesis, University of Edinburgh, 1992. http://hdl.handle.net/1842/15456.

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An investigation into the conformational stability of the small globular protein ubiquitin (Ub) is described. Solid phase peptide synthesis has been successfully applied to the construction of both mammalian ubiquitin, as well as to a ubiquitin analogue (Ubdes-Core) lacking the protein's pronounced hydrophobic core. In each case the synthetic protein was purified to homogeneity using a combination of gel filtration, dialysis and ion exchange chromatography. Synthetic ubiquitin was found to be fully active in a ubiquitin specific in vitro protein conjugation assay, whereas Ubdes-Core was found to be completely inactive. The structure of these two proteins has been studied in some detail. Synthetic ubiquitin possesses an identical crystal and NMR derived solution structure to its natural counterpart. Removal of the hydrophobic core from ubiquitin results in a substantial loss in conformational stability (3.7 kcal mol^-1) and consequently Ubdes-Core is unable to adopt the ubiquitin native fold. This leads to the conclusions that hydrogen bonding contributions are not in themselves sufficient to stabilize the native conformation of ubiquitin. The preparation of a 128 residue precursor protein comprising ubiquitin fused to a C-terminal extension protein (CE-52) is presented along with the CEP52 fragment alone. The compounds were prepared by solid phase peptide synthesis and purified using a combination of gel filtration, ion exchange and HPLC. Two-dimensional NMR analysis of the UbCEP52 precursor revealed, significantly, that it possesses no well defined tertiary structure. However, the protein was found to be processed in vitro to mature ubiquitin and CEP52. A possible novel function of ubiquitin in unfolded C-terminally fused conujugates is suggested.

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Rea, Anita M. "Spectroscopic studies of the protein conformational landscape." Thesis, University of Nottingham, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.517787.

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Apap-Bologna, Angela. "Conformational studies of fibrinogen and its derivatives." Thesis, University of St Andrews, 1988. http://hdl.handle.net/10023/14957.

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There is much controversy regarding the conformation of fibrinogen. Several models have been proposed ranging from a trinodular arrangement to a globular conformation. It has also been suggested that fibrinogen has a flexible structure where the shape of the molecule is influenced by its environment, one major factor being calcium concentration, In addition, although the importance of tightly bound calcium ions (kd 1M) to the fibrinogen molecule is well established, the role of the larger number of low affinity sites (kd 1mM) is still a matter of some debate. In this study, the two techniques of photosensitized radioactive surface labelling and photosensitized cross-linking were selected for development and assessment. This was done with a view to examining the conformation of fibrinogen in its native state and under different solvent conditions, with particular reference to the influence of calcium. The two techniques have been shown to have definite applications in their use as probes into the conformation of fibrinogen. Results derived using these methods support the view put forward by various authors that fibrinogen is a dynamic molecule having a flexible conformation and that the conformation adopted is dependent on solvent composition. Calcium concentration in the millimolar range is particularly significant and consequently so is the saturation of the low affinity binding sites which may well have a regulatory function. Experimentally two extreme conformations have been demonstrated, - a closed, compact structure at low calcium concentrations compared to a more open one at higher calcium concentrations. More importantly, the techniques used also show the subtle changes which occur within the molecule as the calcium concentration is raised, changes which may be more significant physiologically. The most important of these are the effect of calcium on the C-terminal parts of the Aa-chains and the D domains of the molecule.

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Beltran-Sanchez, Marcos. "Synthesis and Conformational Studies of Various Amides." Scholarly Commons, 2019. https://scholarlycommons.pacific.edu/uop_etds/3661.

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In the past, aminocyclohexanol rings have been successfully utilized as pH-triggered molecular switches in various trans-2-aminocyclohexanol derivatives. By changing the groups on the amine nitrogen, these models provided a wide pH range in which a switch can occur. The pH-induced switch of conformation was monitored by 1H-NMR spectroscopy. The models were also incorporated into the bilayer membrane of liposome structures and tested for their ability to disrupt their membrane upon their conformational flip induced by a decrease in pH. In this work, the amide bond has been studied as a molecular switch and various amide derivatives have been tested for their potential as lipid-like compounds that also exhibit a pH-sensitive conformational flip. The conformational analysis of these compounds was achieved by various NMR techniques and NMR acid-base titration studies were utilized to estimate the pKa of a number of the compounds described.

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Lee, Gregory Mitchell. "Solution-state conformational studies of endothelin analogs /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/11619.

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Zhang, Li. "Conformational studies of biologically significant peptide structures /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3001260.

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Hu, Thomas Qiuxiong. "Synthesis and conformational studies of 10, 10-dimethyltridecanolide." Thesis, University of British Columbia, 1988. http://hdl.handle.net/2429/27960.

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The synthesis of 10,10-dimethyltridecanolide (42) was achieved via a fifteen-step sequence in 9% overall yield. The hydrolysis of macrolides 42, 35, and ester 109 was used to probe the conformational behavior of macrolide 42. The results of this study were rationalized through molecular mechanics (MM2) calculations of conformations for macrolide 42. MM2 studies confirmed initial conformational analyses that macrolide 42 should exist predominantly in the [3434] conformation 42a. More importantly, they also revealed the existence of a [3344] conformation 42f. Hydrolysis studies showed that macrolides 42 and 35 hydrolyzed more slowly than ester 109 due to the steric effect of the intermediates. They also suggested that the minor conformation 42f very likely controlled the hydrolysis process of macrolide 42. [Formula Omitted]
Science, Faculty of
Chemistry, Department of
Graduate

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Zaccheus, Mona. "Structural and Conformational Studies of Oligo- and Polysaccharides." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-75050.

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The focus of this thesis is to examine the structural properties of polysaccharides produced by bacteria, as well as the dynamic and conformational behavior of a synthetically derived oligosaccharide. The primary structures of the O-polysaccharide repeating units of four different Escherichia coli (E. coli) strains, namely O175, O177, O103 and TD2158, as well as the first report of a capsular polysaccharide produced by lactic acid bacteria Leuconostoc mesenteroides ssp. cremoris PIA2 are reported in paper I–V. Structural analyses have been performed using a combination of nuclear magnetic resonance spectroscopy and chemical component analysis. The elucidated structures in paper I–III, as well as paper V, are composed of linear repeating units of varying composition and length. In paper IV, the structure of the O-polysaccharide repeating unit of E. coli TD2158 is determined to be a branched hexasaccharide structure with a heterogeneous substitution pattern, with either a β-GlcpNAc or β-Glcp residue branching to the backbone chain. Incubation with bacteriophage HK620 tailspike protein shows that the polysaccharide is selectively cleaved at the α-GlcpNAc-(1→2)-α-Rhap-linkage of the backbone chain, yielding a 9:1 ratio of β-GlcpNAc/β-Glcp containing hexasaccharides after digestion. In paper VI the conformational properties of a trisaccharide, which constitutes an internal epitope of the LeaLex hexasaccharide over-expressed on the surface of squamous lung cancer cells, have been analyzed using NMR spectroscopy and molecular dynamics simulations. The β-(1→3)-linkage of the trisaccharide was shown to be highly flexible.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 6: Submitted.

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Zhang, Yuhui, and 張玉慧. "Beta-Aminoxy peptides as foldamers: synthesisand conformational studies." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B45015259.

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Walford, Gillian. "NMR and conformational studies of bacterial polysaccharide antigens." Thesis, University of Cambridge, 1993. https://www.repository.cam.ac.uk/handle/1810/272377.

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Bryars, Karen Helen. "Synthesis, characterisation and conformational studies of six membered platinacycles." Thesis, University of Warwick, 1988. http://wrap.warwick.ac.uk/99332/.

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Locke, Julie Myree, University of Western Sydney, College of Health and Science, and School of Biomedical and Health Sciences. "Synthetic and conformational studies of hexahydropyrimidines and related heterocycles." THESIS_CHS_BHS_Locke_J.xml, 2003. http://handle.uws.edu.au:8081/1959.7/638.

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This thesis explores the synthesis and conformational behaviour of hexahydropyrimidines and related heterocycles, with particular emphasis on 5- hyrdohexahydropyrimidines. The conformational behaviour of these compounds was investigated using dynamic NMR spectroscopy, molecular modelling techniques and X-ray crystal structure analysis. The conformational behaviour of 5- hyrdohexahydropyrimidine, hexahydropyrimidine and their analogous oxygen compounds as well as a series of hexahydropyrimidines with various exocyclic substituents, were examined. The preferred conformations of all these compounds are attenuated by a combination of steric and electronic influences. These influences include intramolecular hydrogen bonding as well as anomeric and gauche interactions. The conformational behaviour of the selected seven membered benzodiazepine rings, which share structural characteristics with the six-membered 5- hyrdohexahydropyrimidines was also explored. The increased flexibility of the seven membered rings facilitates intramolecular hydrogen bonding, which in turn retards ring inversion in these systems
Doctor of Philosophy (PhD)

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Swarbrick, James David. "Conformational studies of medium-sized molecules by NMR spectroscopy." Thesis, University of Newcastle Upon Tyne, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337191.

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Bartlett, Stephen James. "Synthesis, conformational studies and biological activity of bisindolylmaleimide cyclophanes." Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.424060.

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Chambers, Eric James. "Conformational studies of fluoro- and hydroxy- compounds in solution." Thesis, University of Liverpool, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316776.

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Lee, Imshik. "The conformational and nano-structural image studies of macromolecules." Thesis, University of Bristol, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282573.

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Yuan, Chunhua. "Structural and conformational studies of bovine pancreatic phospholipase A2 /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487948807588005.

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Evenäs, Johan. "NMR studies on calcium-induced conformational transitions in calmodulin." Lund : Lund University, 1998. http://catalog.hathitrust.org/api/volumes/oclc/68945076.html.

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Locke, Julie Myree. "Synthetic and conformational studies of hexahydropyrimidines and related heterocycles." Thesis, View thesis, 2003. http://handle.uws.edu.au:8081/1959.7/638.

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This thesis explores the synthesis and conformational behaviour of hexahydropyrimidines and related heterocycles, with particular emphasis on 5- hyrdohexahydropyrimidines. The conformational behaviour of these compounds was investigated using dynamic NMR spectroscopy, molecular modelling techniques and X-ray crystal structure analysis. The conformational behaviour of 5- hyrdohexahydropyrimidine, hexahydropyrimidine and their analogous oxygen compounds as well as a series of hexahydropyrimidines with various exocyclic substituents, were examined. The preferred conformations of all these compounds are attenuated by a combination of steric and electronic influences. These influences include intramolecular hydrogen bonding as well as anomeric and gauche interactions. The conformational behaviour of the selected seven membered benzodiazepine rings, which share structural characteristics with the six-membered 5- hyrdohexahydropyrimidines was also explored. The increased flexibility of the seven membered rings facilitates intramolecular hydrogen bonding, which in turn retards ring inversion in these systems

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Locke, Julie Myree. "Synthetic and conformational studies of hexahydropyrimidines and related heterocycles /." View thesis, 2003. http://library.uws.edu.au/adt-NUWS/public/adt-NUWS20060517.103404/index.html.

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Thesis (Ph.D.) -- University of Western Sydney, 2003.
"A thesis submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy , University of Western Sydney, Campbelltown, February 2003". Includes references : leaves 188 - 200, and appendices.

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Hodgson, Michael Keith. "Studies of DNA conformation and interaction." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323536.

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Silenzi, Ilaria. "Synthesis, characterization and conformational studies of bis-phenothiazine-aryl-boranes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amslaurea.unibo.it/19201/.

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This thesis project presents a work based on the study of a particular class of amino-boranes, called bis-phenothiazine-aryl-boranes. The peculiarity of these compounds is the N-B-N chemical moiety and their complex conformational behaviour, due to the combination of steric hindrance and conjugation of the B-N bond. Our work is focused on two main products with different symmetry: bis-phenothiazine-2-methylnaphthyl-borane (2b) and bis-phenothiazine-anthracenyl-borane (2c). We firstly focused our attention on an effective way of synthesis, by optimizing both reaction conditions and purification. The products and co-products of interest were then characterized with NMR, mass spectroscopy and X-Ray diffraction on single crystals. The products were eventually analysed through conformational studies, by experimental techniques, such as dynamic NMR and EXSY, and by a theorical approach with DFT calculations.

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Hao, Yu. "Synthesis and conformational studies of beta 2,3-cyclic aminoxy peptides." Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36363236.

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McIntire, Mark Douglas. "Conformational studies of selected phosphines using an empirical computational approach." Virtual Press, 1985. http://liblink.bsu.edu/uhtbin/catkey/444702.

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Conformations of phenyl and alkyl substituted phosphines were studied by using an empirical computer program, CAMSEQ. The computer program employs potential energy functions for calculating non-bonded interactions. The three potential energy functions employed are: steric interactions, represented by Lennard-Jones 6-12 potentials; electrostatic interactions, computed from a Coulomb's Law function; and torsional barriers, approximated by a two-term cosine function. P-C and C-C torsional functions were parameterized for a variety of phosphorus and carbon substituents from published experimental data. Phenyl and alkyl substituent conformations as affected by length, Position and number of alkyl chain substituents are described and related to effective sizes of the phosphines.Ball State UniversityMuncie, IN 47306

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Enjalbal, C. S. "Synthesis and conformational studies of cyclic peptides and their analogues." Thesis, Swansea University, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.636905.

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The first Chapter deals with the biological properties of the RGD motif which has been identified as the recognition site in adhesive interactions between integrin cell surface receptors and extra-cellular glycoproteins such as fibronectin or associated with inhibition of platelet aggregation by snake venom peptides. Chapter II gives an account of structure-activity relationship studies of low molecular weight RGD antagonists which have been reported in the recent literature to probe the structural requirements determining RGD affinity and specificity for integrins. In our approach, a cyclic pentapeptide directly derived from the active site of fibronectin, cyclo[RGDSK], was chosen as model template in an attempt to mimic the putative bioactive structure. Fmoc-t-butyl polyamide solid-phase strategy reviewed briefly in Chapter III was employed for the preparation of the linear precursor which was then cyclized in solution-phase under dilute conditions. Optimization of the synthesis of cyclo[RGDSK] is reported in Chapter IV. The subsequent analogues were designed to improve the bioactivity of the initial template while maintaining its selectivity towards integrins, either by replacing aspartic acid with an unusual residue γ-carboxyglutamic acid (Gla) that binds to integrin calcium sites triggering platelet aggregation, or by inserting the binding motif in a hydrophobic ring. The syntheses of cyclo[RG-DL-Gla-SK] and cyclo[RGDFF] are detailed in Chapter V. Chapter VI deals with the preparation of a depsipeptide mimetic, cyclo[RGD-Phlac_2], designed to increase the backbone flexibility of the last analogue by incorporation of two depside links. Finally, the structural and biological analyses of these cyclopeptides and cyclodepsipeptides discussed in Chapter VII should provide more insights into the active conformation of the RGD motif.

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Hao, Yu, and 郝宇. "Synthesis and conformational studies of beta 2,3-cyclic aminoxy peptides." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B36363236.

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Forrest, Fiona Ruth Ferguson. "Conformational studies on some inhibitors of thermolysin and EC 3.4.24.11." Thesis, University of Glasgow, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.305787.

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39

Lu, Maolin. "Single-Molecule Spectroscopy Studies of the Conformational Dynamics of Enzymes." Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1415118092.

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40

Yamasaki, Masayuki. "Studies on the Conformational Transition of Ovalbumin into Thermostabilized Forms." Kyoto University, 2002. http://hdl.handle.net/2433/149931.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第9645号
農博第1273号
新制||農||847(附属図書館)
学位論文||H14||N3677(農学部図書室)
UT51-2002-G403
京都大学大学院農学研究科応用生命科学専攻
(主査)教授廣瀬正明, 教授池田篤治, 教授北畠直文
学位規則第4条第1項該当

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41

Houseknecht, Justin B. "Conformational Analysis of Furanose Ring Systems: Experimental and Theoretical Studies." Connect to this title online, 2003. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1040404808.

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Thesis (Ph. D.)--Ohio State University, 2003.
Title from first page of PDF file. Document formatted into pages; contains xxiv, 529 p.; also includes graphics Includes bibliographical references (p. 510-529). Available online via OhioLINK's ETD Center

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42

Angelici, Gaetano <1979&gt. "De Novo Design of secondary structures: Synthesis and conformational studies." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1352/1/Gaetano_Angelici_Tesi_di_Dottorato.pdf.

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Chemists have long sought to extrapolate the power of biological catalysis and recognition to synthetic systems. These efforts have focused largely on low molecular weight catalysts and receptors; however, biological systems themselves rely almost exclusively on polymers, proteins and RNA, to perform complex chemical functions. Proteins and RNA are unique in their ability to adopt compact, well-ordered conformations, and specific folding provides precise spatial orientation of the functional groups that comprise the “active site”. These features suggest that identification of new polymer backbones with discrete and predictable folding propensities (“foldamers”) will provide a basis for design of molecular machines with unique capabilities. The foldamer approach complements current efforts to design unnatural properties into polypeptides and polynucleotides. The aim of this thesis is the synthesis and conformational studies of new classes of foldamers, using a peptidomimetic approach. Moreover their attitude to be utilized as ionophores, catalysts, and nanobiomaterials were analyzed in solution and in the solid state. This thesis is divided in thematically chapters that are reported below. It begins with a very general introduction (page 4) which is useful, but not strictly necessary, to the expert reader. It is worth mentioning that paragraph I.3 (page 22) is the starting point of this work and paragraph I.5 (page 32) isrequired to better understand the results of chapters 4 and 5. In chapter 1 (page 39) is reported the synthesis and conformational analysis of a novel class of foldamers containing (S)-β3-homophenylglycine [(S)-β3-hPhg] and D- 4-carboxy-oxazolidin-2-one (D-Oxd) residues in alternate order is reported. The experimental conformational analysis performed in solution by IR, 1HNMR, and CD spectroscopy unambiguously proved that these oligomers fold into ordered structures with increasing sequence length. Theoretical calculations employing ab initio MO theory suggest a helix with 11-membered hydrogenbonded rings as the preferred secondary structure type. The novel structures enrich the field of peptidic foldamers and might be useful in the mimicry of native peptides. In chapter 2 cyclo-(L-Ala-D-Oxd)3 and cyclo-(L-Ala-DOxd) 4 were prepared in the liquid phase with good overall yields and were utilized for bivalent ions chelation (Ca2+, Mg2+, Cu2+, Zn2+ and Hg2+); their chelation skill was analyzed with ESI-MS, CD and 1HNMR techniques and the best results were obtained with cyclo-(L-Ala-D-Oxd)3 and Mg2+ or Ca2+. Chapter 3 describes an application of oligopeptides as catalysts for aldol reactions. Paragraph 3.1 concerns the use of prolinamides as catalysts of the cross aldol addition of hydroxyacetone to aromatic aldeydes, whereas paragraphs 3.2 and 3.3 are about the catalyzed aldol addition of acetone to isatins. By means of DFT and AIM calculations, the steric and stereoelectronic effects that control the enantioselectivity in the cross-aldol addition of acetone to isatin catalysed by L-proline have been studied, also in the presence of small quantities of water. In chapter 4 is reported the synthesis and the analysis of a new fiber-like material, obtained from the selfaggregation of the dipeptide Boc-L-Phe-D-Oxd-OBn, which spontaneously forms uniform fibers consisting of parallel infinite linear chains arising from singleintermolecular N-H···O=C hydrogen bonds. This is the absolute borderline case of a parallel β-sheet structure. Longer oligomers of the same series with general formula Boc-(L-Phe-D-Oxd)n-OBn (where n = 2-5), are described in chapter 5. Their properties in solution and in the solid state were analyzed, in correlation with their attitude to form intramolecular hydrogen bond. In chapter 6 is reported the synthesis of imidazolidin-2- one-4-carboxylate and (tetrahydro)-pyrimidin-2-one-5- carboxylate, via an efficient modification of the Hofmann rearrangement. The reaction affords the desired compounds from protected asparagine or glutamine in good to high yield, using PhI(OAc)2 as source of iodine(III).

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43

Angelici, Gaetano <1979&gt. "De Novo Design of secondary structures: Synthesis and conformational studies." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1352/.

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Chemists have long sought to extrapolate the power of biological catalysis and recognition to synthetic systems. These efforts have focused largely on low molecular weight catalysts and receptors; however, biological systems themselves rely almost exclusively on polymers, proteins and RNA, to perform complex chemical functions. Proteins and RNA are unique in their ability to adopt compact, well-ordered conformations, and specific folding provides precise spatial orientation of the functional groups that comprise the “active site”. These features suggest that identification of new polymer backbones with discrete and predictable folding propensities (“foldamers”) will provide a basis for design of molecular machines with unique capabilities. The foldamer approach complements current efforts to design unnatural properties into polypeptides and polynucleotides. The aim of this thesis is the synthesis and conformational studies of new classes of foldamers, using a peptidomimetic approach. Moreover their attitude to be utilized as ionophores, catalysts, and nanobiomaterials were analyzed in solution and in the solid state. This thesis is divided in thematically chapters that are reported below. It begins with a very general introduction (page 4) which is useful, but not strictly necessary, to the expert reader. It is worth mentioning that paragraph I.3 (page 22) is the starting point of this work and paragraph I.5 (page 32) isrequired to better understand the results of chapters 4 and 5. In chapter 1 (page 39) is reported the synthesis and conformational analysis of a novel class of foldamers containing (S)-β3-homophenylglycine [(S)-β3-hPhg] and D- 4-carboxy-oxazolidin-2-one (D-Oxd) residues in alternate order is reported. The experimental conformational analysis performed in solution by IR, 1HNMR, and CD spectroscopy unambiguously proved that these oligomers fold into ordered structures with increasing sequence length. Theoretical calculations employing ab initio MO theory suggest a helix with 11-membered hydrogenbonded rings as the preferred secondary structure type. The novel structures enrich the field of peptidic foldamers and might be useful in the mimicry of native peptides. In chapter 2 cyclo-(L-Ala-D-Oxd)3 and cyclo-(L-Ala-DOxd) 4 were prepared in the liquid phase with good overall yields and were utilized for bivalent ions chelation (Ca2+, Mg2+, Cu2+, Zn2+ and Hg2+); their chelation skill was analyzed with ESI-MS, CD and 1HNMR techniques and the best results were obtained with cyclo-(L-Ala-D-Oxd)3 and Mg2+ or Ca2+. Chapter 3 describes an application of oligopeptides as catalysts for aldol reactions. Paragraph 3.1 concerns the use of prolinamides as catalysts of the cross aldol addition of hydroxyacetone to aromatic aldeydes, whereas paragraphs 3.2 and 3.3 are about the catalyzed aldol addition of acetone to isatins. By means of DFT and AIM calculations, the steric and stereoelectronic effects that control the enantioselectivity in the cross-aldol addition of acetone to isatin catalysed by L-proline have been studied, also in the presence of small quantities of water. In chapter 4 is reported the synthesis and the analysis of a new fiber-like material, obtained from the selfaggregation of the dipeptide Boc-L-Phe-D-Oxd-OBn, which spontaneously forms uniform fibers consisting of parallel infinite linear chains arising from singleintermolecular N-H···O=C hydrogen bonds. This is the absolute borderline case of a parallel β-sheet structure. Longer oligomers of the same series with general formula Boc-(L-Phe-D-Oxd)n-OBn (where n = 2-5), are described in chapter 5. Their properties in solution and in the solid state were analyzed, in correlation with their attitude to form intramolecular hydrogen bond. In chapter 6 is reported the synthesis of imidazolidin-2- one-4-carboxylate and (tetrahydro)-pyrimidin-2-one-5- carboxylate, via an efficient modification of the Hofmann rearrangement. The reaction affords the desired compounds from protected asparagine or glutamine in good to high yield, using PhI(OAc)2 as source of iodine(III).

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44

Billsten, Peter. "Studies on the conformation of adsorbed proteins." Lund : Göteborg University, 1997. http://catalog.hathitrust.org/api/volumes/oclc/39776983.html.

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45

Foschi, Simone. "Synthesis, Characterization and Conformational Studies of Modified Carbazole-bis-aryl-boranes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2020. http://amslaurea.unibo.it/20686/.

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During this project we have synthetized different compounds belonging to the class of amino-boranes for the study of bis-aryl-B=N system. We have decided to keep unchanged the aryl components and change only the amine to observe the effect of that on the B=N bond. The used amines are modified carbazoles with functional groups chosen to amplify or disempower the steric and the conjugation effect. We have found that the evaluation of steric barrier was possible studying the gearing aryls rotation around the C-B bonds, while the conjugation barrier is instead given by the energy needed to break the formal double bond B=N and allow the amine rotation. The work started with a proposed synthesis, improved for every reaction, then the products are characterized by NMR, fluorometric spectroscopy, mass spectrometry and X-Ray diffraction on single crystal. The following study on rotational energy barrier was possible theoretically through DFT calculation and experimentally with techniques like Dynamic NMR and EXSY. The fluorometric analysis was done for the study of the solvatochromic propriety of the products.

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46

Östervall, Jennie. "Conformational Dynamics of Carbohydrates Studied by NMR Spectroscopy and Molecular Simulations." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1023.

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Carbohydrates play important roles in biological processes. Their function is closely related to their conformation. In this thesis, conformational studies of carbohydrates by NMR spectroscopy and molecular dynamics computer simulations are described. The first two papers discuss the anomalous solubility of β-cyclodextrin compared to other cyclodextrins. Time correlation functions revealed flexibility in all cyclodextrins. Molecular dynamics computer simulations showed that the glycosidic linkages were rather rigid and the flexibility was suggested to be macrocyclic. From spatial distribution functions β-cyclodextrin was found to have greater ability to order the surrounding water than the other cyclodextrins. Paper III deals with some of the difficulties of conformational studies. In Paper IV, a new method, Additative Potential Maximum Entropy, APME, is applied to a disaccharide. Conformational distribution functions are derived from NOEs, J-couplings and residual dipolar couplings and calculated from computer simulations. All distribution functions were found to be in good agreement. In papers V and VI oligosaccharides from human milk are studied. Residual dipolar coupling, J-couplings and cross relaxation rates were measured by NMR spectroscopy and molecular dynamics computer simulations were carried out. Both oligosaccharides showed high flexibility for the β-D-GlcpNAc-(1→3)-β-D-Galp linkage.

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47

Östervall, Jennie. "Conformational dynamics of carbohydrates studied by NMR spectroscopy and molecular simulations /." Stockholm : Department of Organic Chemistry, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1023.

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48

Hadden, Jonathan Mark. "Protein structure and conformational changes studied by Fourier transform infrared spectroscopy." Thesis, University College London (University of London), 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.565953.

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Fourier transform infrared spectroscopy (FTIR) has been used to study a range of different proteins. These include:- i) Human serum transferrin, human lactoferrin and rabbit serum transferrin. A study has been made of the structural changes that accompany iron binding and release from these related proteins. Structural variations within this group of proteins have been shown. Thermal denaturation studies, using differential scanning calorimetric measurements, have been related to FTIR spectral changes and indicate that the crystal structure of iron-free human lactoferrin may not reflect the structure of this protein in solution. ii) Human placental transferrin receptor. This protein has been examined at extracellular and endosomal pH. Both the intact protein in detergent and its water soluble major extracellular fragment have been investigated. iii) The bacterial adhesive protein streptococcal antigen I/II. The solution structure and thermal stability of the native protein, the recombinant full-length protein and four recombinant fragments of this protein have been examined using both Fourier transfonn infrared spectroscopy and circular dichroism spectroscopy. iv) Albumin, IgG, Ribonuclease, Fibrinogen. A study of the thermal stability of these and other proteins has been undertaken to compare their denaturation properties in H20 and 2H20 solutions. v) Lysozyme, Ribonuclease. These and several other proteins have been examined using Fourier transfonn infrared microscopy in order to compare the infrared spectra of these proteins, both in solution and also in the fonn of single crystals. Many of the proteins show similar spectra, whether recorded in solution or from a single crystal. In some cases, as with single crystals of Endothia parasitica pepsin, Mucor pucillus pepsin and serum amyloid P component, the spectra differ from those recorded in solution. These differences may indicate that a rearrangement of turns structures occurs upon crystallisation. The major novel findings of this work are: i) There are small but significant structural differences between human serum transferrin, rabbit serum transferrin and human lactoferrin. The crystal structure of human lactoferrin may not represent the structure of this protein in solution. The apparent conflict between CD, FTIR and X-ray crystallographic estimates of secondary structural content of the transferrins can be explained by the fact that CD estimates are based on dihedral angles and not hydrogen bonding patterns. ii) Intact transferrin receptor precipitates out of solution at endosomal pH while the extracellular fragment remains soluble but undergoes a confonnational change. This results in minor change in the secondary structural content of the protein and a reduction of thennal stabi lity by approximately 15°C. iii) The recombinant polypeptides produced to study the structure of streptococcal antigen IIII have been shown to fold into defined secondary structures. Furthermore the structures of these fragments have been used to predict a possible structure for the native protein. iv) Quantitative analysis of thermally induced changes in the FTIR spectra of proteins in H20 solution may not offer any significant advantage to analyses performed in 2H20 due to problems associated with the different molar absorption coefficients of the separate secondary structures in H20 solution. v) Infrared spectroscopy/microscopy can be successfully be applied to the study of protein structure in both the solution and crystalline form.

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49

Gray, Geoffrey M. "Conformational Fluctuations of Biomolecules Studied Using Molecular Dynamics and Enhanced Sampling." Scholar Commons, 2018. http://scholarcommons.usf.edu/etd/7156.

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Biomolecule structural fluctuations determine function, regulating numerous biological processes My research has shed light on several interesting cases in which structural fluctuations have been identified to assess functional differences. Chapter 2 discusses the effects of structural rearrangement of the β2-β3 loop on the DNA binding affinity of the type 6 human papillomavirus E2 protein. Chapter 3 investigates the effects of phosphorylation on the C-terminal domain of Cdc37, a protein important in the Hsp90 chaperone cycle. Chapter 4 studies the effects on cyclycization on the conformational fluctuations of a γ-AApeptide used for high-throughput libraries. Chapter 5 is a structural study on a mini-fibril of spider dragline silk, in which a native-like ensemble was generated using temperature replica exchange. Chapter 6 investigates the structural features of repetitive motifs found in spider dragline silk when subject to both dope-like and fiber-like conditions. Chapter 7 elucidates conformational differences between the RXRα and the RXRβ ligand-binding domains and seeks to understand the atomic basis for different ligand binding affinities. This body of work has contributed to the understanding of conformational fluctuations and changes that occur in protein-DNA binding systems, drug-binding, regulation of chaperones via post-translations modifications and spider dragline silk.

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50

Timol, Zaheer. "Chemical and conformational studies of bacterial cell surface polysaccharide repeating units." Master's thesis, University of Cape Town, 2017. http://hdl.handle.net/11427/25484.

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Abstract Bacterial cell surface polysaccharides are primarily present as lipopolysaccharides or capsular polysaccharides. They are used by cells for both structure and function and have been shown to be a virulence factor of bacterial pathogens. Cell surface polysaccharides are widely utilised as antigenic components in vaccines and play an important role in the protection against numerous diseases including meningococcal disease and shigellosis. This study is composed of two parts: a computational section, which investigates the capsular polysaccharide (CPS) repeating unit (RU) conformations of meningococcal Y and W CPS vaccines and a second experimental component that involves synthetic studies toward the O-specific polysaccharide (O-SP) RU of Shigella sonnei. The CPS RU of MenY [→6)-α-D-Glc(1→4)-α-D-NeuNAc-(2→] and MenW [→6)-α-D-Gal(1→4)-α-D-NeuNAc-(2→] differ only in the orientation of the C-4 hydroxyl: equatorial in MenY and axial in MenW. However, groups Y and W CPS vaccines have different levels of antibody cross-protection. The purpose of the computational study was to determine if these observed differences may be attributed to CPS RU conformation. Potential of mean force calculations were applied to disaccharide RUs of MenY and MenW, and larger three repeating units (3RU) were simulated with molecular dynamics (MD) in solution. The molecular modelling showed that differences in RU conformation between the meningococcal groups arise primarily due to the structural differences between glucose and galactose; affecting the behaviour and orientation of the 2→6 dihedral linkage. The 2→6 linkages in the MenY 3RU adopt a single preferred orientation and consequently it has a single dominant molecular conformation. In contrast, the 2→6 linkages in the MenW 3RU move frequently between different rotameric conformations resulting in multiple conformational families. These results indicate significant conformational differences between the MenY and MenW CPS RUs, which may account for the different levels of cross-protection observed. The synthetic component was part of a larger study to develop a novel route towards the O-SP RU of S. sonnei for use in biological testing and physicochemical characterisation for vaccine development. The O-SP RU of S. sonnei is →4-α-L-AltNAc-(1→3)-β-D-FucNAc4N(1→. The multi-step synthesis was performed using known methodology as well as methods developed by the research group. The key 2,3-oxazolidinone protected intermediate was successfully synthesised in good yields and due to time constraints the final product synthesised was two steps away from the protected FucNAc4N residue. Additional studies were performed on the 2,3-oxazolidinone intermediate as part of a divergent synthesis strategy toward the AltNAcA residue of S. sonnei. Reactions were conducted whereby β and α derivatives of the 2,3-oxazolidinone intermediate were successfully synthesised in large scale and good yields for further studies to be performed by the group. i

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