Dissertations / Theses on the topic '3D crystal structure'

Lipoxygenases (LOX) catalyze regio- and stereospecific oxygenation of polyunsaturated fatty acids to hydroperoxides. These hydroperoxides are further metabolized to leukotrienes and lipoxins in mammals, and are involved in asthma and inflammation. LOX of animals and plants contain iron as catalytic metal (FeLOX). Filamentous fungi use both FeLOX, and manganese containing LOX (MnLOX). The role of LOX in fungi is still not known. This thesis focuses on expression of novel MnLOX, analyses of their reaction mechanism and products by HPLC-MS/MS, protein crystallization and analysis of the first MnLOX structure.   MnLOX from G. graminis, M. salvinii, M. oryzae, F. oxysporum and C. gloeosporioides were expressed in Pichia pastoris, purified and characterized by HPLC-MS/MS. All MnLOX catalyzes suprafacial hydrogen abstraction and oxygen insertion. Replacement of one Ile to Phe in the active site of MnLOX of G. graminis could switch the mechanism from suprafacial to mainly antarafacial. MnLOX of F. oxysporum was interesting since it catalyzes oxygenation of linoleic acid to 11R- instead of the more common 11S-hydroperoxides. This feature could be attributed to a single Ser/Phe exchange in the active site.   We found that Gg-MnLOX utilizes hydrogen tunneling in the reaction mechanism, but was slightly more temperature dependent than soybean FeLOX. It is an intriguing question why some fungal LOX use manganese and not iron as catalytic metal and whether the large redox potential of Mn2+/Mn3+ (1.5 V) can be tuned close to that of Fe2+/Fe3+ (0.77 V) for redox cycling and catalysis. We present crystallization conditions for two MnLOX, and the 2.07 Å crystal structure of MnLOX from M. oryzae, solved using sulfur and manganese single anomalous dispersion (SAD). The structure reveals a similar metal coordinating sphere as FeLOX but the metal ligand Asn473 was positioned on a short loop instead of a helix and formed interactions with a conserved Gln. This feature could be essential for the use of manganese as catalytic metal in LOX. We found three Phe residues that likely facilitate the suprafacial hydrogen abstraction and oxygen insertion for MnLOX. These findings provide new insight into the unique reaction mechanism of MnLOX.

Eksperimentai buvo atliekami su bandinėliais gautais iš Madrido, Maskvos ir St.Peterburgo, tai yra su fotoniniais kristalais. Darbe buvo nagrinėta fotoninio kristalo opalo struktūrą ir optines savybes draustinės stop juostos srityje bei defektų valdymo būdai, keičiant elektrinį lauką. Nagrinėjamas elektrinio lauko poveikis defektams, stop juostai. Nustatyta, kad elektriniame lauke susikuria defektai, kuriuos galima valdyti nuo 0V iki 7V įtampos intervale. Išmatuoti defektinės modos perjungimo laikai kurie sieka 200 s, tai 10 kart greičiau nei stop juostos.
We did structural and spectroscopic studies of bulk and thin film synthetic opal. Demonstrate that the photonic crystal, opal have defects, but these defects may be "good" when use it to control light in stop band.

Les glutathion transférases (GSTs) constituent une famille multigénique d’enzymes ubiquitaires impliquées notamment dans la détoxication des xénobiotiques et le métabolisme secondaire. Les GSTs canoniques sont constituées d’un domaine N-terminal de type thiorédoxine et d’un domaine C-terminal formé d’hélices α. Chez les plantes terrestres, les GSTs peuvent être regroupées en 14 classes et selon le résidu conservé au sein de leur motif catalytique en GSTs à cystéine (Cys-GSTs) ou à sérine (Ser-GSTs). Les Ser-GSTs présentent des activités de réduction des peroxydes et/ou de conjugaison de glutathion (GSH) alors que les Cys-GSTs portent des activités de déglutathionylation et déshydroascorbate réductase. Certaines d’entre elles présentent également des propriétés non-catalytiques de type ligandine à des fins de transport ou de stockage de molécules diverses. Les GSTs Tau (GSTUs) correspondent à la classe regroupant le plus d’isoformes chez les plantes et leur sont spécifiques. Les GSTUs sont souvent surexprimées lors de stress biotiques et abiotiques et participent notamment à la détoxication des herbicides. Toutefois, le rôle physiologique des GSTUs reste encore lacunaire in planta. En combinant des approches phylogénétiques, biochimiques et structurales, ces travaux ont conduit à la caractérisation de neuf GSTUs d’Arabidopsis thaliana (AtGSTUs) et de six GSTUs de Populus trichocarpa (PtGSTUs). L’analyse phylogénétique des Ser-GSTs d’organismes photosynthétiques a révélé que l’expansion des GSTUs est apparue de façon concomitante à l’apparition du réseau vasculaire chez les plantes bien que quelques mousses et bryophytes possèdent des GSTUs. Au sein d’un organisme, les GSTUs peuvent être classées en groupes distincts en fonction de leur motif catalytique. Les essais enzymatiques réalisés ont montré que quasiment toutes les GSTUs d’intérêt portent des activités de conjugaison du GSH et de réduction des peroxydes envers différents substrats modèles (CDNB, dérivés d’isothiocyanates, hydroperoxydes). Les structures tridimensionnelles de deux GSTUs ont été résolues et ces dernières présentent le repliement classique des GSTs canoniques avec des différences notables entre elles. Les analyses biochimiques et structurales réalisées sur les protéines AtGSTUs et PtGSTUs d’intérêt ont montré que certaines d’entre elles lient des porphyrines bactériennes et d’autres des composés polyphénoliques. Parmi les complexes enzyme-ligand identifiés, la structure d’un complexe baicaléine-GSTU a été résolue. L’utilisation d’échantillons enrichis en métabolites extraits de plantes représente la prochaine étape sur le chemin de l’analyse fonctionnelle des GSTUs
Glutathione transferases (GSTs) constitute a ubiquitous multigene superfamily of enzymes involved in xenobiotic detoxification and secondary metabolism. Canonical GSTs consist of an N-terminal thioredoxin domain and a α-helical C-terminal domain. In terrestrial plants, GSTs can be grouped in 14 classes but also according to the conserved residue found in their catalytic site either cysteine (Cys-GSTs) or serine (Ser-GSTs) GSTs. Ser-GSTs exhibit reduction of peroxides and/or glutathione (GSH) conjugation activities while Cys-GSTs rather exhibit deglutathionylation and dehydroascorbate reductase activities. Some of them also appear to have non-catalytic ligandin properties for the transport or storage of various molecules. The plant-specific Tau GST (GSTU) class is usually the most expanded one. The GSTUs are often over-expressed during biotic and abiotic stresses contributing notably to herbicide detoxification. However, the physiological role of most GSTUs is still poorly documented in planta. By combining phylogenetic, biochemical and structural approaches, this work led to the characterisation of nine GSTUs from Arabidopsis thaliana (AtGSTUs) and six GSTUs from Populus trichocarpa (PtGSTUs). Phylogenetic analysis of the Ser-GSTs present in photosynthetic organisms revealed that the expansion of GSTUs occurred concomitantly with the appearance of vasculature in plants, although some mosses and bryophytes possess GSTUs. Within an organism, GSTUs can be classified into distinct groups according to their catalytic motif. Enzymatic tests using recombinant proteins showed that almost all studied GSTUs exhibit GSH conjugation and peroxide reduction activities against different model substrates (CDNB, isothiocyanate derivatives, hydroperoxides). The three-dimensional structures of two GSTUs have been resolved and these adopt the classical canonical GST fold with some notable difference between them. The biochemical and structural analyses of these AtGSTUs and PtGSTUs further showed that some of them bind bacterial porphyrins while others bind polyphenolic compounds. Among the enzyme-ligand complexes identified, the structure of a bacalein-GSTU has been solved. The use of metabolites enriched samples extracted from A. thaliana and P. trichocarpa is the next step to decipher the role of GSTUs in planta

Optical resonators are structures that allow light to circulate and store energy for a duration of time. This work primarily looks at the fabrication, characterization, and application of whispering gallery mode microresonators and the analysis of organic photonic crystal-like structures and simulation of their resonant effects. Whispering gallery mode (WGM) microresonators are a class of cylindrically symmetric optical resonator which light circulates around the equator of the structure. These resonators are named after acoustic whispering galleries, where a whisper can be heard anywhere along the perimeter of a circular room. These optical structures are known for their ultra high Q-factor and their low mode volume. Q-factor describes the photon lifetime in the cavity and is responsible for the energy buildup within the cavity and sharp spectral characteristics of WGM resonators. The energy buildup is ideal for non-linear optics and the sharp spectral features are beneficial for sensing applications. Characterization of microbubble resonators is done by coupling light from a tunable laser source via tapered optical fiber into the cavity. The fabrication of quality tapered optical fiber on the order of 1-2 μm is critical to working on WGM resonators. The measurement of Q-factors up to 2x10⁸ and mode spectra are possible with these resonators and experimental techniques. This work focuses on microdisk and microbubble WGM resonators. The microdisk resonators are fabricated by femtosecond laser micromachining. The micromachined resonators are fabricated by ablating rotating optical fiber to generate the disk shape and then heated to reflow the surface to improve optical quality. These resonators have a spares mode spectrum and display a Q factor as high as 2x10⁶. The microbubble resonators are hollow microresonators fabricated by heating a pressurized capillary tube which forms a bubble in the area exposed to heat. These have a wall thickness of 2-5 μm and a diameter of 200-400 μm. Applications in pressure sensing and two-photon fluorescence of dye in microbubble resonators is explored. Photonic crystals can have engineered resonant properties by tuning photonic band gaps and introducing defects to create cavities in the photonic structure. In this work, a natural photonic crystal structure is analyzed in the form of diatoms. Diatoms are a type of phytoplankton which are identified by unique ornamentation of each species silica shell, called a frustule. The frustule is composed of a quasi-periodic lattice of pores which closely resembles manmade photonic crystals. The diatom frustules are analyzed using image processing techniques to determine pore-to-pore spacing and identify defects in the quasi-periodic structure which may contribute to optical filtering and photonic band gap effects. The data gathered is used to simulate light propagation through the diatom structure at different incident angles and with different material properties and to verify data gathered experimentally.

Ce travail porte sur l’étude d’une nouvelle technique de microscopie basée sur le phénomène d’absorption linéaire ultra-faible (LOPA) de matériaux photosensibles pour la fabrication de structures submicrométriques à deux et à trois dimensions (2D, 3D). Premièrement, nous avons étudié théoriquement la distribution de l'intensité lumineuse dans la région focale d’un objectif de microscope de grande ouverture numérique en fonction des différentes conditions de travail, telles que la propagation de la lumière dans un milieu absorbant avec variation d'indice de refraction. Nous avons démontré que lorsque l'on travaille avec un matériau quasi homogène ayant de très faible absorption à la longueur d’onde du faisceau d’excitation, le faisceau laser peut être focalisé en profondeur à l'intérieur du matériau, ce qui permet de manipuler optiquement des objets en 3D. Nous avons ensuite démontré expérimentalement l'utilisation de cette technique pour fabriquer des structures à la demande. Différentes structures 2D et 3D submicrométriques ont été crées en résine SU-8, en utilisant un laser continue de faible puissance à 532 nm. Ces résultats sont similaires à ceux obtenus par la méthode d’absorption à deux photons, mais le coût de fabrication a été énormément réduit. De plus, nous avons démontré qu'il est possible de fabriquer des structures photoniques à base de polymère contenant une seule nanoparticule (NP), en utilisant un procédé à deux étapes. En effet, nous avons d'abord déterminé avec précision la position d'une seule NP d’or, en utilisant une puissance d’excitation très faible, puis nous l'avons insérée dans une structure photonique par une puissance d’excitation plus élevée. Le couplage d'une NP d’or et d'une structure photonique à base de polymère a été ensuite étudié théoriquement et expérimentalement, montrant une amélioration importante de la collection des photons émis par la NP
This work deals with a novel microscopy technique based on the ultra-low one-photon absorption (LOPA) mechanism of photosensitive materials for fabrication of arbitrary two- and three-dimensional (2D, 3D) submicrometer structures. First, we theoretically investigated the intensity distribution at focusing region of a high numerical aperture objective lens as a function of various working conditions, such as propagation of light mismatched refractive index and/or absorbing media. We demonstrated that when working with refractive index mismatch-free and very low absorption conditions, the light could be focused deeply inside the material, allowing a 3D optical manipulation. We then demonstrated experimentally the use of this simple technique for fabrication of desired structures. Different 2D and 3D structures, with a feature as small as 150 nm, have been created in SU-8 photoresist by using a low power and continuous-wave laser emitting at 532 nm. Furthermore, we demonstrated that it is possible to fabricate a polymer-based photonic structure containing a single nanoparticle (NP), by using a double-step method. Indeed, the LOPA microscopy allowed us first to accurately determine the location of a single gold NP and then to embed it as desired into an arbitrary SU-8 photonic structure. The coupling of a gold NP and a polymer-based photonic structure was theoretically and experimentally investigated showing a six-fold photons collection enhancement as compared to that of a NP in unpatterned film

In the late eighties, a new class of materials, known as photonic crystals (PCs), emerged enabling the propagation and generation of light to be potentially manipulated with unprecedented control. PCs consist of a periodic modulation of dielectric constant in one, two, or three dimensions, which can result in the formation of directional or omni-directional photonic band gaps (PBGs), spectral regions where light propagation is forbidden, and more remarkably, novel dispersion characteristics. Since PC properties scale with the dimension of the wavelength of interest, significant technological constraints must be fully addressed to manufacture 3D PBG materials for optical or infrared applications such as displays, lightning, and communications. PCs enable the unraveling of unique optical phenomena such as PBGs, spontaneous emission rate manipulation, sub-wavelength focusing, and superprism effects. This research focuses on the feasibility to achieve omni-directional PBGs in synthetic opal-based 3D PCs through precise nanoscale control to the original dielectric architecture. In particular, the optical response to the conformal deposition of dielectric layers using atomic layer deposition (ALD) within the porous template is strongly emphasized. Geometrical models were developed to faithfully model the manipulation of the synthetic opal architecture by ALD and then used in electromagnetic algorithms to predict the resulting optical properties. From these results, this research presents and investigates a scheme used to greatly enhance and adjust the PBG width and position, as well as simultaneously reducing the dielectric contrast threshold at which the PBG forms. This Thesis demonstrates that the unique opal architectures offered by ALD not only supports the formation of larger PBGs with high index materials; but also enables the use of optically transparent materials with reduced refractive index. Additionally, slight alteration of these structures facilitates the incorporation of non-linear (NL) electro-optical (EO) material for dynamic tuning capabilities and potentially offers a pathway for fabricating multi-functional photonic devices. Finally, low-temperature ALD was investigated as a means to manipulate band gaps and dispersion effects in 2D PC silicon slab waveguides and 3D organic biologically-derived templates. The results indicate the unique ability of ALD to achieve composite structures with desirable (large PBGs) or novel (slow light) optical properties.

碩士
國立臺灣大學
光電工程學研究所
95
In the past ten years, photonic crystal fibers (PCFs) have been widely researched. This special type of fibers, with two-dimensional periodic cladding, provides many impressive properties, such as large mode area, endlessly single mode, etc. Recently, PCFs with periodic modulation in the transmission direction are also developed, increasing the periodicity from 2D to 3D. In literature, 3D structure PCFs have been used as fiber gratings and are more efficient than common fibers because of their larger index difference in constitute material. In this thesis, CO2 laser was employed to periodically modulate the diameter of PCF. There are some advantages to fabricate 3D structure PCF by laser heated pedestal growth (LHPG) system: First, many UV-induced gratings will degrade by time, and the Ge doping in core destroys the original physical properties of the fiber. In contrast, the grating fabricated by CO2 laser is stable even in high temperature. Second, the common laser-heated system always heats the fiber in one or two directions, which may induce larger birefringence effect. The ring heating design of our LHPG system has higher symmetry than any other laser-heated system in literature, which may reduce local collapse of the hole structures in PCF and maintain the transmission characteristics. Two methods, periodical control of shutter or motor stages, were used to fabricate 3D structure PCF with about 224.25 micron pitch. The fabricated structure served as a notch filter and the peak attenuation of 16 dB at 1557.5 nm was achieved. Numerical simulations based on a commercially available beam propagation method (BPM) software and coupled-mode theory were used to model the 3D structure PCF. The simulated result agrees well with our fabricated 3D structure PCF.

碩士
國立成功大學
化學系碩博士班
97
The assembly of heterometallic 3d-4f ions and organic ligands, 6-(5-carboxypyridin-2-ylthio)pyridine-3-carboxylate ([S(C5H3NCO2)2]2-, TIN) and 3-mercaptopropionate ((2OCC2H4S)2-, TPC), have successfully constructed a series of metal-organic frameworks by the solventhermal reactions. Single-crystal structures, elemental analyses, infrared records, and magnetic behavior were characterized for these compounds. Six compounds possessing the same structure were discovered in the series of [Cu12Ln2(H2O)2(TPC)6Cl6]．4H2O where Ln denotes Nd(1), Eu(2), Gd(3), Tb(4), Dy(5), and Er(6). Unique [Cu12S6] clusters, rhombic [Gd2O2] units are formed in this structure, which are interconnected by TPC ligands. Within the cluster, known as Altas-sphere, twelve Cu+ ions are fused together through μ4-S atoms. The [Cu12S6] clusters are bridged together by Cl– ions into a network with square-like windows. The networks are then supported by the [Gd2O2] units into an open framework in 3, where water molecules are encapsulated within the tunnels along the a axis. The magnetic study of Gd compound displays interesting ferromagnetic behavior at the low temperature that phenomenon could be caused by the asymmetric geometry of the [Gd2O2] units. The compound GdCu2(H2O)2(TIN)3Cl (7) crystallizes into a new network. First, the 1D zigzag chains are formed by [CuN4Cl] and [CuN2O3] units, which are alternatively connected through TIN ligands. Further, the chains are fused together with Gd3+ ions by another two distinct sites of TIN ligands to form the 2D layer in 7. The network are packing by ��-�� interactions along the a axis.

No
Decaprenylphosphoryl-b-d-ribose 20-epimerase (DprE1) is a potential drug target for development of antitubercular agents. Structure based drug discovery approach yielded twenty novel derivatives of benzothiazolylpyrimidine-5-carboxamides (7a–t) which were synthesised by three component one pot reaction involving benzothiazolyl oxobutanamide, thiourea and substituted aromatic benzaldehydes. These derivatives were evaluated for antitubercular activity to determine MIC and compound 7a, 7e, 7f and 7o were found to be potentially active against Mycobacterium tuberculosis (H37Rv). Log P of these compounds was found to be between 2.0 and 3.0 making them suitable for oral dosing. DprE1 selectivity and pharmacokinetic studies were carried out for these compounds of which 7a and 7o were found to be highly selective and bioavailability was found to be above 52% by oral dose. Crystal structure of 7a was studied and molecular packing was determined, it exhibited a triclinic crystal lattice arrangement having hydrogen bonded dimeric arrangement. Drug receptor interactions were studied which exhibited docking in the active site of receptor with hydrogen bonding, hydrophobic interactions, vdW interactions with amino acid residues such as Cys387, Asn385, Lys418, Tyr314, Gln334 and Lys367 respectively. 3D QSAR analysis was carried out by kNN-MFA method to determine and develop theoretical model, best suitable model was found to be based on Simulated Annealing k-Neariest Neighbour Molecular Field Analysis (SA kNN-MFA). The model provided with hydrophobic descriptors in positive side indicating the need of bulky groups, steric and electronegative descriptors in negative coordinates hints with contribution by the electronegative substitutions as favourable and desirable moieties for enhancing the activity. The q2, q2_se and Pred_r2se were found to be 0.5000, 0.6404 and 1.0094 respectively. A pharmacophore model was generated which suggested for necessity of aromatic, aliphatic carbon centre and hydrogen bond donor for development of newer DprE1 selective inhibitors.
Council of Scientific and Industrial Research

Transition metal compounds present a unique class of solids with complex and diverse thermodynamic properties. 3d transition metal oxides exist with a great variety of crystal structures, which are reflected in the richness of their physical properties. The orbital states of 3d electrons are to a large extent responsible for the complex relationship between the electronic properties and crystal structure. This complexity and diversity are the indication of strong interplay between electronic, lattice, orbital and spin degrees of freedom. The magnetic ground states of these oxides depend strongly on the environment surrounding the transition metal and also on the exchange interaction pathways between two magnetic ions, which is often mediated through the 2p levels of oxygen. The thesis entitled “Study of magnetic and dielectric properties of 3d transition metal oxides” is devoted to the experimental investigations focusing the magnetic and electric properties of some exotic transition metal oxides with fascinating crystal structures. Where necessary, the X-ray photo-electron spectroscopy, temperature dependent XRD have also been studied to have a comprehensive understanding of the systems. In many cases experimental results are fitted to the existing theoretical models to clarify the analysis. All the results and analyses based on the investigations performed during this tenure have been included in this thesis along with the theoretical background and experimental methodologies.
The research was carried out under the supervision of Prof. Subham Majumdar of Solid State Physics division under SPS [School of Physical Sciences]
The research was conducted under IACS fellowship

碩士
國立臺灣大學
光電工程學研究所
106
Blue phase liquid crystal display is a popular research topic for the liquid crystal display. Because of its sub-millisecond response time and its display without alignment layer that make it be fabricated easier. However, the primary problems of blue phase liquid crystal are low transmittance and high operating voltage. Many theses aim to design different electrode structures to improve the high operating voltage and low transmittance. Most theses aim to design two-dimension electrode structures about parameters on X-Z direction. Therefore, we design the three-dimension electrode structures and hope that new structures can reduce the dead zone on y-direction. At first, we refer to three kinds of 2D electrode structures to design three kinds of 3D electrode structures. We discover that 3D electrodes have the problem of central dead zone and the problem influence the transmittance of the display. After the analysis, the 2D electrodes still have the highest transmittance. However, 3D electrodes also have their advantage. 3D electrodes have higher transmittance at low operating voltage if the electrode gap is small. Then we refer to Diamond-shape electrodes to design continuous electrodes to reduce the central dead zone on expectation so we compare continuous electrodes with Diamond-shape electrodes first. The result is that the pointed diamond electrodes have higher transmittance in comparison with Diamond-shape electrodes generally ( ). The enhanced Diamond electrodes have higher transmittance and lower operation voltage in comparison with Diamond-shape electrodes. In the end, we compare continuous electrodes with 2D and 3D electrodes. Among 2D, 3D triangle and pointed diamond electrodes, 2D triangle electrodes have the highest transmittance with large gap but 3D triangle electrodes have the higher transmittance at low voltage with small gap. Pointed diamond electrodes have high transmittance over 75% with most electrode gaps. Among 2D, 3D enhanced trapezoid and enhanced diamond electrodes, 2D enhanced trapezoid electrodes have the highest transmittance with large gap but 3D enhanced trapezoid electrodes have the higher transmittance at low voltage with small gap. Enhanced diamond electrodes have high transmittance over 80% with most electrode gaps. In terms of transmittance vs electrode gaps, continuous electrodes combine the features of 2D and 3D electrodes. Continuous electrodes have less sensitivity on electrode gaps compared to 2D and 3D electrodes with reasonably high transmittance.

The high resolution structure of protein molecules and protein-protein complexes is important to investigate their functions. Today, large 3D or 2D crystals are required to obtain protein structures by X-ray crystallography or conventional Electron Microscopy, respectively. However, production of such crystals of good quality is a solely empirical procedure, which relies on screening numerous crystallization conditions. At the same time, multilayered protein crystals are often a by-product of attempts to grow 3D or 2D crystals and could be obtained more easily. So far, multilayered protein crystals have not been used in electron microscopy for structure determination, as the interpretation of an electron diffraction pattern is rather complicated. In this thesis we present the first protein structure bovine liver catalase at 4 Å resolution solved using electron diffraction data from multilayered crystals. 55 diffraction patterns (17 tilt series) were recorded and used for the reconstruction. The tilt geometry of each individual diffraction pattern was determined by a least-squares algorithm or Laue zone analysis to perform spot indexing. The phase problem was solved by molecular replacement. The influence of the missing data cone on the self-rotation function and interpretation of reconstructed map is discussed.