Succinate:ubiquinone oxidoreductase from Paracoccus denitrificans and particulate methane monooxygenase from Methylococcus capsulatus (Bath): experimental and theoretical EPR studies of the metal cofactors

This thesis summarizes the application of conventional and modern electron paramagnetic resonance (EPR) techniques to establish proximity relationships between paramagnetic metal centers in metalloproteins and between metal centers and magnetic ligand nuclei in two important and timely membrane proteins: succinate:ubiquinone oxidoreductase (SQR) from Paracoccus denitrificans and particulate methane monooxygenase (pMMO) from Methylococcus capsulatus. Such proximity relationships are thought to be critical to the biological function and the associated biochemistry mediated by the metal centers in these proteins. A mechanistic understanding of biological function relies heavily on structure-function relationships and the knowledge of how molecular structure and electronic properties of the metal centers influence the reactivity in metalloenzymes. EPR spectroscopy has proven to be one of the most powerful techniques towards obtaining information about interactions between metal centers as well as defining ligand structures. SQR is an electron transport enzyme wherein the substrates, organic and metallic cofactors are held relatively far apart. Here, the proximity relationships of the metallic cofactors were studied through their weak spin-spin interactions by means of EPR power saturation and electron spin-lattice (T_1) measurements, when the enzyme was poised at designated reduction levels. Analysis of the electron T_1 measurements for the S-3 center when the b-heme is paramagnetic led to a detailed analysis of the dipolar interactions and distance determination between two interacting metal centers. Studies of ligand environment of the metal centers by electron spin echo envelope modulation (ESEEM) spectroscopy resulted in the identication of peptide nitrogens as coupled nuclei in the environment of the S-1 and S-3 centers.

Finally, an EPR model was developed to describe the ferromagnetically coupled trinuclear copper clusters in pMMO when the enzyme is oxidized. The Cu(II) ions in these clusters appear to be strongly exchange coupled, and the EPR is consistent with equilateral triangular arrangements of type 2 copper ions. These results offer the first glimpse of the magneto-structural correlations for a trinuclear copper cluster of this type, which, until the work on pMMO, has had no precedent in the metalloprotein literature. Such trinuclear copper clusters are even rare in synthetic models.

Homo- and Heteronuclear Transition Metal Complexes Supported by Multinucleating Ligands

This dissertation is mainly divided into two sub-parts: organometallic and bioinorganic/materials projects. The approach for the projects involves the use of two different multinucleating ligands to synthesize mono- and multinuclear complexes. Chapter 2 describes the synthesis of a multinucleating tris(phosphinoaryl)benzene ligand used to support mono-nickel and palladium complexes. The isolated mononuclear complexes were observed to undergo intramolecular arene C¬–H to C–P functionalization. The transformation was studied by nuclear magnetic resonance spectroscopy and X-ray crystallography, and represents a rare type of C–H functionalization mechanism, facilitated by the interactions of the group 10 metal with the arene π–system.

Chapter 3 describes the construction of multinickel complexes supported by the same triphosphine ligand from Chapter 2. This chapter shows how the central arene in the ligand’s triarylbenzene framework can interact with dinickel and trinickel moieties in various binding modes. X-ray diffraction studies indicated that all compounds display strong metal–arene interactions. A cofacial triangulo nickel(0) complex supported by this ligand scaffold was also isolated and characterized. This chapter demonstrates the use of an arene as versatile ligand design element for small molecular clusters.

Chapter 4 presents the syntheses of a series of discrete mixed transition metal Mn oxido clusters and their characterization. The synthesis of these oxide clusters displaying two types of transition metals were targeted for systematic metal composition-property studies relevant to mixed transition metal oxides employed in electrocatalysis. A series of heterometallic trimanganese tetraoxido cubanes capped with a redox-active metal [MMn₃O₄] (M = Fe, Co, Ni, Cu) was synthesized starting from a [CaMn₃O₄] precursor and structurally characterized by X-ray crystallography and anomalous diffraction to conclusively determine that M is incorporated at a single position in the cluster. The electrochemical properties of these complexes were studied via cyclic voltammetry. The redox chemistry of the series of complexes was investigated by the addition of a reductant and oxidant. X-ray absorption and electron paramagnetic resonance spectroscopies were also employed to evaluate the product of the oxidation/reduction reaction to determine the site of electron transfer given the presence of two types of redox-active metals. Additional studies on oxygen atom transfer reactivities of [MMn₃O₄] and [MMn₃O₂] series were performed to investigate the effect of the heterometal M in the reaction rates.

Chapter 5 focuses on the use of [CoMn₃O₄] and [NiMn₃O₄] cubane complexes discussed in Chapter 4 as precursors to heterogeneous oxygen evolution reaction (OER) electrocatalysts. These well-defined complexes were dropcasted on electrodes with/without heat treatment, and the OER activities of the resulting films were evaluated. Multiple spectroscopic techniques were performed on the surface of the electrocatalysts to gain insight into the structure-function relationships based on the heterometallic composition. Depending on film preparation, the Co-Mn-oxide was found to change metal composition during catalysis, while the Ni-Mn oxide maintained the NiMn3 ratio. These studies represent the use of discrete heterometallic-oxide clusters as precursors for heterogeneous water oxidation catalysts.

Appendix A describes the ongoing effort to synthesize a series of heteromultimetallic [MMn₃X] clusters (X = O, S, F). Complexes such as [ZnMn₃O], [CoMn₃O], [Mn₃S], and [Mn₄F] have been synthesized and structurally characterized. An amino-bis-oxime ligand (PRABO) has been installed on the [ZnMn₃O] cluster. Upon the addition of O₂, the desymmetrized [ZnMn₃O] cluster only underwent an outer-sphere, one-electron oxidation. Efforts to build and manipulate other heterometallic [MMn₃X] clusters are still ongoing, targeting O₂ binding and reduction. Appendix B summarizes the multiple synthetic approaches to build a [Co₄O₄]-cubane complex relevant to heterogeneous OER electrocatalysis. Starting with the tricobalt cluster [LCo₃(O₂CR)₃] and treatment various strong oxidants that can serve as oxygen atom source in the presence Co²⁺ salt only yielded tricobalt mono–oxo complexes. Appendix C presents the efforts to model the H-cluster framework of [FeFe]-hydrogenase by incorporating a synthetic diiron complex onto a protein-supported or a synthetic ligand-supported [Fe₄S₄]-cluster. The mutant ferredoxin with a [Fe₄S₄]-cluster and triscarbene ligand have been characterized by multiple spectroscopic techniques. The reconstruction of an H-cluster mimic has not yet been achieved, due to the difficulty of obtaining crystallographic evidence and the ambiguity of the EPR results.

DNA-mediated charge transport signaling within the cell

DNA possesses the curious ability to conduct charge longitudinally through the π-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.

Herein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.

In separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?

UvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters.

LiMn2-xGexO4 como material catódico para baterías de ión-litio

32 p.

Codoping Na+ to modulate the spectroscopy and photoluminescence properties of Yb3+ in CaF2 laser crystal

kinds of Yb3+- and Na+-codoped CaF2 laser crystal with different Na:Yb ratios of 0, 1.5, and 10 are grown by the temperature gradient technique. Room-temperature absorption, photoluminescence spectra, and fluorescence lifetimes belonging to the transitions between ground state F-2(7/2) and excited state F-2(5/2) of Yb3+ ions in the three crystals are measured to study the effect of Na+. Experimental results show that codoping Na+ ions in different Na:Yb ratios can modulate the spectroscopy and photoluminescence properties of Yb3+ ions in a CaF2 lattice in a large scope. (c) 2005 Optical Society of America

Sites structure and spectroscopic properties of Yb-doped and Yb, Na-codoped CaF2 laser crystals

For the first time, the effect of Na+ on crystal structure, valence state of Yb ions, spectroscopic properties of YbF3-doped CaF2 system was systematically studied. Na+ can greatly suppress the deoxidization of Yb3+ to Yb2+. Absorption and emission spectra showed codoping Na+ with different Na:Yb ratios can modulate the spectroscopy and photoluminescence properties of Yb3+ ions in CaF2 lattice in a large scope. The emission lifetime and quantum efficiency of Yb3+ in CaF2 were greatly enhanced by the codopant of Na+. The potential laser performances of the new Yb, Na-codoped CaF2 crystals were predicted. (c) 2005 Elsevier B.V. All rights reserved.

Dehydration for a solid coordination network based on CuII-(py)2C(OH)2 trimers

Abstract de congreso: Póster presentado en 12th International Conference on Materials Chemistry (MC12), 20 - 23 July 2015, York, United Kingdom

利用DSC和EPR技术研究杜仲种子的贮藏条件

种子贮藏稳定性对于种质资源的长期保存具有重要意义，目前关于种子贮藏的最新理论为玻璃态理论，该理论认为种子的玻璃化有利于种子的长期贮藏。当种子处于玻璃态时，玻璃化物质的高度粘滞性降低了种子细胞内分子流动性，阻止了细胞质中分子的扩散，从而减少老化过程中细胞结构的损伤和化学组分的变化，延缓种子老化劣变反应速率，延长贮藏寿命。评价玻璃态的一个重要指标是玻璃化转变温度，当种子贮藏于玻璃化温度或以下10℃～30℃范围内时，种子具有最佳的贮藏稳定性。因此，检测种子的玻璃化转变温度对于种子的长期有效贮藏具有重要指导意义。 本研究将差示量热扫描技术（DSC）与电子顺磁共振波谱仪技术（EPR）应用于杜仲种子玻璃化转变温度方面的研究。在DSC方法中，选用4.4%～31.6%含水量范围的杜仲种胚分别进行了DSC图谱扫描。EPR方法选用3-羧基-2,2,5,5-四甲基吡咯烷-1-氧（3-carboxy-2,2,5,5-tetramethylpyrrolidine-1-oxyl，CP）和2,2,6,6-四甲基哌啶（4-hydroxy-2,2,6,6-tetramethyl-1-piperidinyloxy，TEMPO）作为探针标记杜仲种胚， 利用EPR技术测定不同含水量杜仲种胚的分子运动，通过对EPR图谱参数的分析计算，最终确定不同含水量杜仲种胚的玻璃化转变温度。 DSC实验结果显示，含水量为22.3%、28.0%、31.6%的杜仲种胚在0℃ 左右出现了一个水的熔融峰。该熔融峰的面积代表了自由水含量的多少，随着种胚含水量的降低该熔融峰面积减小。4.4%～31.6%含水量范围的杜仲种胚在-28℃左右还出现了一个熔融峰，推测此峰为杜仲种胚中某类物质熔融所形成的熔融峰。然而在此曲线上我们未观察到标志玻璃化转变的“台阶”出现。 CP-EPR实验的结果表明，利用EPR测定得到含水量为4.4%～11.6%的杜仲种胚在-110℃～20℃温度范围内，同一含水量的杜仲种胚随着温度的升高，分子运动速率加快;在同一温度条件下，高含水量的种胚比低含水量种胚的分子运动速率快。通过CP-EPR波谱两外缘峰最大距离（2Azz）的测定和数据统计分析，得到含水量为4.4%、5.7%、8.6%、10.3%、11.6%杜仲种胚的玻璃化转变温度分别约为44℃、25℃、4℃、-31℃、-43℃。可以把测定的杜仲种胚的这几个含水量的玻璃化转变温度与杜仲种子贮藏相结合，用于指导杜仲种子的贮藏。 TEMPO-EPR实验测定分析得到含水量为2.1%、3.4%、4.8%、8.3%、11.2% 的杜仲种胚的玻璃化转变温度分别为-21℃、-18℃、-24℃、-20℃、-27℃，玻璃化转变温度随含水量升高其变化的规律不明显，这与CP-EPR实验测得的结果有着较明显的差别。通过分析，认为对于脂质含量较高的杜仲种胚，随着含水量的降低，作为标记化合物的TEMPO随着脱水进入脂相，从而不能真实反映出不同含水量种胚的分子运动情况。与TEMPO标记相比，CP标记可能能够更真实地反映不同含水量杜仲种胚细胞质分子运动的情况，根据其分子运动情况得到的玻璃化转变温度更准确。

Radiation hardness improvement of separation-by-implantation-of-oxygen/silicon-on-insulator material by nitrogen ion implantation

In our work, nitrogen ions were implanted into separation-by-implantation-of-oxygen (SIMOX) wafers to improve the radiation hardness of the SIMOX material. The experiments of secondary ion mass spectroscopy (SIMS) analysis showed that some nitrogen ions were distributed in the buried oxide layers and some others were collected at the Si/SiO2 interface after annealing. The results of electron paramagnetic resonance (EPR) suggested the density of the defects in the nitrided samples changed with different nitrogen ion implantation energies. Semiconductor-insulator-semiconductor (SIS) capacitors were made on the materials, and capacitance-voltage (C-V) measurements were carried out to confirm the results. The super total dose radiation tolerance of the materials was verified by the small increase of the drain leakage current of the metal-oxide-semiconductor field effect transistor with n-channel (NMOSFETs) fabricated on the materials before and after total dose irradiation. The optimum implantation energy was also determined.

Research on nitrogen implantation energy dependence of the properties of SIMON materials

With different implantation energies, nitrogen ions were implanted into SIMOX wafers in our work. And then the wafers were subsequently annealed to form separated by implantation of oxygen and nitrogen (SIMON) wafers. Secondary ion mass spectroscopy (SIMS) was used to observe the distribution of nitrogen and oxygen in the wafers. The result of electron paramagnetic resonance (EPR) was suggested by the dandling bonds densities in the wafers changed with N ions implantation energies. SIMON-based SIS capacitors were made. The results of the C-V test confirmed that the energy of nitrogen implantation affects the properties of the wafers, and the optimum implantation energy was determined. (c) 2005 Elsevier B.V. All rights reserved.

Research on nitrogen implantation energy dependence of the properties of SIMON materials

With different implantation energies, nitrogen ions were implanted into SIMOX wafers in our work. And then the wafers were subsequently annealed to form separated by implantation of oxygen and nitrogen (SIMON) wafers. Secondary ion mass spectroscopy (SIMS) was used to observe the distribution of nitrogen and oxygen in the wafers. The result of electron paramagnetic resonance (EPR) was suggested by the dandling bonds densities in the wafers changed with N ions implantation energies. SIMON-based SIS capacitors were made. The results of the C-V test confirmed that the energy of nitrogen implantation affects the properties of the wafers, and the optimum implantation energy was determined. (c) 2005 Elsevier B.V. All rights reserved.

THEORETICAL INVESTIGATION OF THE DYNAMIC PROCESS OF THE ILLUMINATION OF GAAS

The dynamic process of light illumination of GaAs is studied numerically in this paper to understand the photoquenching characteristics of the material. This peculiar behavior of GaAs is usally ascribed to the existence of EL2 states and their photodriven metastable states. To understand the conductivity quenching, we have introduced nonlinear terms describing the recombination of the nonequilibrium free electrons and holes into the calculation. Though some photoquenching such as photocapacitance, infrared absorption, and electron-paramagnetic-resonance quenching can be explained qualitatively by only considering the internal transfer between the EL2 state and its metastability, it is essential to take the recombination into consideration for a clear understanding of the photoquenching process. The numerical results and approximate analytical approach are presented in this paper for the first time to our knowledge. The calculation gives quite a reasonable explanation for n-type semiconducting GaAs to have infrared absorption quenching while lacking photoconductance quenching. Also, the calculation results have allowed us to interpret the enhanced photoconductance phenomenon following the conductance quenching in typical semi-insulating GaAs and have shown the expected thermal recovery temperature of about 120 K. The numerical results are in agreement with the reported experiments and have diminished some ambiguities in previous works.

PHOTOINDUCED CHANGES OF HYDROGEN-BONDING IN SEMIINSULATING IRON-DOPED INDIUM-PHOSPHIDE

After illumination with 1-1.3 eV photons during cooling-down, metastable PH modes are observed by IR absorption at 5 K in semi-insulating InP:Fe. They correlate with the photo-injection of holes, but not with a change of the charge state of the K-related centres present at equilibrium. They are explained by a change of the bonding of H, induced by hole trapping, from IR-inactive centres to PH-containing centres, stable only below 80 K. One metastable centre has well-defined geometrical parameters and the other one could be located in a region near from the interface with (Fe,P) precipitates.

A mechanism for enhanced photocatalytic activity of silver-loaded titanium dioxide

In this paper, silver-loaded TiO2 photocatalyst was prepared by photochemical impregnation method and characterized by transmission electron microscopy (TEM), diffuse reflectance spectra (DRS), photooxidation of phenol and photoreduction of Cr(VI). Electron paramagnetic resonance (EPR) was used to detect photoproduced paramagnetic radicals. The correlation of photocatalytic activity and photogenerated reactive species was discussed, and the mechanism of silver-loaded TiO2 for enhancement of photocatalytic activity was elucidated. The results show that deposited silver on TiO2 Surface acts as a site where electrons accumulate. The better separation between electrons and holes on the modified TiO2 surface allowed more efficiency for the oxidation and reduction reactions. The enhanced photocatalytic activity was mainly attributed to the increased amounts of O-2(.-) reactive species and surface Ti3+ reactive center on silver-loaded TiO2 photocatalyst. (C) 2004 Published by Elsevier B.V.

The enhancement of TiO2 photocatalytic activity by hydrogen thermal treatment

In this study, conventional TiO2 powder was heated in hydrogen (H-2) gas at a high temperature as pretreatment. The photoactivity of the treated TiO2 samples was evaluated in the photodegradation of sulfosalicylic acid (SSA) in aqueous suspension. The experimental results demonstrated that the photodegradation rates of SSA were significantly enhanced by using the H-2-treated TiO2 catalysts and an optimum temperature for the H-2 treatment was found to be of 500-600 degreesC. The in situ electron paramagnetic resonance (EPR) signal intensity of oxygen vacancies (OV) and trivalent titanium (Ti3+) associated with the photocatalytic activity was studied. The results proved the presence of OV and Ti3+ in the lattice of the H2-treated TiO2 and indicated that both were contributed to the enhancement of photocatalytic activity. Moreover, the experimental results presented that the EPR signal intensity of OV and Ti3+ in the H-2-treated TiO2 samples after 10 months storage was still significant higher than that in the untreated TiO2 catalyst. The experiment also demonstrated that the significant enhancement occurred in the photodegradation of phenol using the H-2-treated TiO2. (C) 2002 Elsevier Science Ltd. All rights reserved.