Surface Studies of Thiolate Adsorbates on Some Metals

The results and discussions in this thesis are based on my studies about selfassembled thiol layers on gold, platinum, silver and copper surfaces. These kinds of layers are two-dimensional, one molecule thick and covalently organized at the surface. They are an easy way to modify surface properties. Self-assembly is today an intensive research field because of the promise it holds for producing new technology at nanoscale, the scale of atoms and molecules. These kinds of films have applications for example, in the fields of physics, biology, engineering, chemistry and computer science. Compared to the extensive literature concerning self-assembled monolayers (SAMs) on gold, little is known about the structure and properties of thiolbased SAMs on other metals. In this thesis I have focused on thiol layers on gold, platinum, silver and copper substrates. These studies can be regarded as a basic study of SAMs. Nevertheless, an understanding of the physical and chemical nature of SAMs allows the correlation between atomic structure and macroscopic properties. The results can be used as a starting point for many practical applications. X-ray photoelectron spectroscopy (XPS) and synchrotron radiation excited high resolution photoelectron spectroscopy (HR-XPS) together with time-offlight secondary ion mass spectrometry (ToF-SIMS) were applied to investigate thin organic films formed by the spontaneous adsorption of molecules on metal surfaces. Photoelectron spectroscopy was the main method used in these studies. In photoelectron spectroscopy, the sample is irradiated with photons and emitted photoelectrons are energy-analyzed. The obtained spectra give information about the atomic composition of the surface and about the chemical state of the detected elements. It is widely used in the study of thin layers and is a very powerful tool for this purpose. Some XPS results were complemented with ToF-SIMS measurements. It provides information on the chemical composition and molecular structure of the samples. Thiol (1-Dodecanethiol, CH3(CH2)11SH) solution was used to create SAMs on metal substrates. Uniform layers were formed on most of the studied metal surfaces. On platinum, surface aligned molecules were also detected in investigations by XPS and ToF-SIMS. The influence of radiation on the layer structure was studied, leading to the conclusion that parts of the hydrocarbon chains break off due to radiation and the rest of the layer is deformed. The results obtained showed differences depending on the substrate material. The influence of oxygen on layer formation was also studied. Thiol molecules were found to replace some of the oxygen from the metal surfaces.

Familial predisposition to hypertension and the association between urinary sodium excretion and blood pressure in a population-based sample of young adults

The reasons for the inconsistent association between salt consumption and blood pressure levels observed in within-society surveys are not known. A total of 157 normotensive subjects aged 18 to 35 years, selected at random in a cross-sectional population-based survey, answered a structured questionnaire. They were classified as strongly predisposed to hypertension when two or more first-degree relatives had a diagnosis of hypertension. Anthropometric parameters were obtained and sitting blood pressure was determined with aneroid sphygmomanometers. Sodium and potassium excretion was measured by flame spectrophotometry in an overnight urine sample. A positive correlation between blood pressure and urinary sodium excretion was detected only in the group of individuals strongly predisposed to hypertension, both for systolic blood pressure (r = 0.51, P<0.01) and diastolic blood pressure (r = 0.50, P<0.01). In a covariance analysis, after controlling for age, skin color and body mass index, individuals strongly predisposed to hypertension who excreted amounts of sodium above the median of the entire sample had higher systolic and diastolic blood pressure than subjects classified into the remaining conditions. The influence of familial predisposition to hypertension on the association between salt intake and blood pressure may be an additional explanation for the weak association between urinary sodium excretion and blood pressure observed in within-population studies, since it can influence the association between salt consumption and blood pressure in some but not all inhabitants.

Extracting Ramachandran torsional angle distributions from 2D NMR data using Tikhonov regularization /

Solid state nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for studying structural and dynamical properties of disordered and partially ordered materials, such as glasses, polymers, liquid crystals, and biological materials. In particular, twodimensional( 2D) NMR methods such as ^^C-^^C correlation spectroscopy under the magicangle- spinning (MAS) conditions have been used to measure structural constraints on the secondary structure of proteins and polypeptides. Amyloid fibrils implicated in a broad class of diseases such as Alzheimer's are known to contain a particular repeating structural motif, called a /5-sheet. However, the details of such structures are poorly understood, primarily because the structural constraints extracted from the 2D NMR data in the form of the so-called Ramachandran (backbone torsion) angle distributions, g{^,'4)), are strongly model-dependent. Inverse theory methods are used to extract Ramachandran angle distributions from a set of 2D MAS and constant-time double-quantum-filtered dipolar recoupling (CTDQFD) data. This is a vastly underdetermined problem, and the stability of the inverse mapping is problematic. Tikhonov regularization is a well-known method of improving the stability of the inverse; in this work it is extended to use a new regularization functional based on the Laplacian rather than on the norm of the function itself. In this way, one makes use of the inherently two-dimensional nature of the underlying Ramachandran maps. In addition, a modification of the existing numerical procedure is performed, as appropriate for an underdetermined inverse problem. Stability of the algorithm with respect to the signal-to-noise (S/N) ratio is examined using a simulated data set. The results show excellent convergence to the true angle distribution function g{(j),ii) for the S/N ratio above 100.

Grain size analyses in tin-lead glazes based on 2d-sections

A problem in the archaeometric classification of Catalan Renaissance pottery is the fact, that the clay supply of the pottery workshops was centrally organized by guilds, and therefore usually all potters of a single production centre produced chemically similar ceramics. However, analysing the glazes of the ware usually a large number of inclusions in the glaze is found, which reveal technological differences between single workshops. These inclusions have been used by the potters in order to opacify the transparent glaze and to achieve a white background for further decoration. In order to distinguish different technological preparation procedures of the single workshops, at a Scanning Electron Microscope the chemical composition of those inclusions as well as their size in the two-dimensional cut is recorded. Based on the latter, a frequency distribution of the apparent diameters is estimated for each sample and type of inclusion. Following an approach by S.D. Wicksell (1925), it is principally possible to transform the distributions of the apparent 2D-diameters back to those of the true three-dimensional bodies. The applicability of this approach and its practical problems are examined using different ways of kernel density estimation and Monte-Carlo tests of the methodology. Finally, it is tested in how far the obtained frequency distributions can be used to classify the pottery

Identification of metabolites in human hepatic bile using 800 MHz 1H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS

The first application of high field NMR spectroscopy (800 MHz for 1H observation) to human hepatic bile (as opposed to gall bladder bile) is reported. The bile sample used for detailed investigation was from a donor liver with mild fat infiltration, collected during organ retrieval prior to transplantation. In addition, to focus on the detection of bile acids in particular, a bile extract was analysed by 800 MHz 1H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS. In the whole bile sample, 40 compounds have been assigned with the aid of two-dimensional 1H–1H TOCSY and 1H–13C HSQC spectra. These include phosphatidylcholine, 14 amino acids, 10 organic acids, 4 carbohydrates and polyols (glucose, glucuronate, glycerol and myo-inositol), choline, phosphocholine, betaine, trimethylamine-N-oxide and other small molecules. An initial NMR-based assessment of the concentration range of some key metabolites has been made. Some observed chemical shifts differ from expected database values, probably due to a difference in bulk diamagnetic susceptibility. The NMR spectra of the whole extract gave identification of the major bile acids (cholic, deoxycholic and chenodeoxycholic), but the glycine and taurine conjugates of a given bile acid could not be distinguished. However, this was achieved by HPLC-NMR/MS, which enabled the separation and identification of ten conjugated bile acids with relative abundances varying from approximately 0.1% (taurolithocholic acid) to 34.0% (glycocholic acid), of which, only the five most abundant acids could be detected by NMR, including the isomers glycodeoxycholic acid and glycochenodeoxycholic acid, which are difficult to distinguish by conventional LC-MS analysis. In a separate experiment, the use of UPLC-MS allowed the detection and identification of 13 bile acids. This work has shown the complementary potential of NMR spectroscopy, MS and hyphenated NMR/MS for elucidating the complex metabolic profile of human hepatic bile. This will be useful baseline information in ongoing studies of liver excretory function and organ transplantation.

Desenvolvimento de método por cromatografia líquida bidimensional abrange para documentação química de extratos vegetais e estudos metabolômicos

Pós-graduação em Química - IQ

Propriedades luminescentes de polioxometalato contendo európio(III) correlacionadas à sua conformação em sólido estendido e em filmes auto-organizados de Langmuir e Langmuir-Blodgett

Pós-graduação em Química - IQ

Infinite dimensional Lie algebra associated with conformal transformations of the two-point velocity correlation tensor from isotropic turbulence

We deal with homogeneous isotropic turbulence and use the two-point velocity correlation tensor field (parametrized by the time variable t) of the velocity fluctuations to equip an affine space K3 of the correlation vectors by a family of metrics. It was shown in Grebenev and Oberlack (J Nonlinear Math Phys 18:109–120, 2011) that a special form of this tensor field generates the so-called semi-reducible pseudo-Riemannian metrics ds2(t) in K3. This construction presents the template for embedding the couple (K3, ds2(t)) into the Euclidean space R3 with the standard metric. This allows to introduce into the consideration the function of length between the fluid particles, and the accompanying important problem to address is to find out which transformations leave the statistic of length to be invariant that presents a basic interest of the paper. Also we classify the geometry of the particles configuration at least locally for a positive Gaussian curvature of this configuration and comment the case of a negative Gaussian curvature.

Heteronuclear recoupling methods in solid-state NMR

This thesis is focused on the development of heteronuclear correlation methods in solid-state NMR spectroscopy, where the spatial dependence of the dipolar coupling is exploited to obtain structural and dynamical information in solids. Quantitative results on dipolar coupling constants are extracted by means of spinning sideband analysis in the indirect dimension of the two-dimensional experiments. The principles of sideband analysis were established and are currently widely used in the group of Prof. Spiess for the special case of homonuclear 1H double-quantum spectroscopy. The generalization of these principles to the heteronuclear case is presented, with special emphasis on naturally abundant 13C-1H systems. For proton spectroscopy in the solid state, line-narrowing is of particular importance, and is here achieved by very-fast sample rotation at the magic angle (MAS), with frequencies up to 35 kHz. Therefore, the heteronuclear dipolar couplings are suppressed and have to be recoupled in order to achieve an efficient excitation of the observed multiple-quantum modes. Heteronuclear recoupling is most straightforwardly accomplished by performing the known REDOR experiment, where pi-pulses are applied every half rotor period. This experiment was modified by the insertion of an additional spectroscopic dimension, such that heteronuclear multiple-quantum experiments can be carried out, which, as shown experimentally and theoretically, closely resemble homonuclear double-quantum experiments. Variants are presented which are well-suited for the recording of high-resolution 13C-1H shift correlation and spinning-sideband spectra, by means of which spatial proximities and quantitative dipolar coupling constants, respectively, of heteronuclear spin pairs can be determined. Spectral editing of 13C spectra is shown to be feasible with these techniques. Moreover, order phenomena and dynamics in columnar mesophases with 13C in natural abundance were investigated. Two further modifications of the REDOR concept allow the correlation of 13C with quadrupolar nuclei, such as 2H. The spectroscopic handling of these nuclei is challenging in that they cover large frequency ranges, and with the new experiments it is shown how the excitation problem can be tackled or circumvented altogether, respectively. As an example, one of the techniques is used for the identification of a yet unknown motional process of the H-bonded protons in the crystalline parts of poly(vinyl alcohol).

Sample preparation of culture medium from Madin-Darby canine kidney cells

A reproducible, standardized and simple sample preparation methodology is the key to successful two-dimensional gel electrophoresis (2-DE). This chapter describes step-by-step the sample preparation of culture medium from Madin-Darby canine kidney (MDCK) cells. Tips and tricks are given to circumvent possible pitfalls.

Three-dimensional imaging methods for quantitative analysis of facial soft tissues and skeletal morphology in patients with orofacial clefts: a systematic review.

BACKGROUND Current guidelines for evaluating cleft palate treatments are mostly based on two-dimensional (2D) evaluation, but three-dimensional (3D) imaging methods to assess treatment outcome are steadily rising. OBJECTIVE To identify 3D imaging methods for quantitative assessment of soft tissue and skeletal morphology in patients with cleft lip and palate. DATA SOURCES Literature was searched using PubMed (1948-2012), EMBASE (1980-2012), Scopus (2004-2012), Web of Science (1945-2012), and the Cochrane Library. The last search was performed September 30, 2012. Reference lists were hand searched for potentially eligible studies. There was no language restriction. STUDY SELECTION We included publications using 3D imaging techniques to assess facial soft tissue or skeletal morphology in patients older than 5 years with a cleft lip with/or without cleft palate. We reviewed studies involving the facial region when at least 10 subjects in the sample size had at least one cleft type. Only primary publications were included. DATA EXTRACTION Independent extraction of data and quality assessments were performed by two observers. RESULTS Five hundred full text publications were retrieved, 144 met the inclusion criteria, with 63 high quality studies. There were differences in study designs, topics studied, patient characteristics, and success measurements; therefore, only a systematic review could be conducted. Main 3D-techniques that are used in cleft lip and palate patients are CT, CBCT, MRI, stereophotogrammetry, and laser surface scanning. These techniques are mainly used for soft tissue analysis, evaluation of bone grafting, and changes in the craniofacial skeleton. Digital dental casts are used to evaluate treatment and changes over time. CONCLUSION Available evidence implies that 3D imaging methods can be used for documentation of CLP patients. No data are available yet showing that 3D methods are more informative than conventional 2D methods. Further research is warranted to elucidate it.

Dielectrophoretic approaches to sample preparation and analysis

Dielectrophoresis (DEP) has been used to manipulate cells in low-conductivity suspending media using AC electrical fields generated on micro-fabricated electrode arrays. This has created the possibility of performing automatically on a micro-scale more sophisticated cell processing than that currently requiring substantial laboratory equipment, reagent volumes, time, and human intervention. In this research the manipulation of aqueous droplets in an immiscible, low-permittivity suspending medium is described to complement previous work on dielectrophoretic cell manipulation. Such droplets can be used as carriers not only for air- and water-borne samples, contaminants, chemical reagents, viral and gene products, and cells, but also the reagents to process and characterize these samples. A long-term goal of this area of research is to perform chemical and biological assays on automated, micro-scaled devices at or near the point-of-care, which will increase the availability of modern medicine to people who do not have ready access to large medical institutions and decrease the cost and delays associated with that lack of access. In this research I present proofs-of-concept for droplet manipulation and droplet-based biochemical analysis using dielectrophoresis as the motive force. Proofs-of-concept developed for the first time in this research include: (1) showing droplet movement on a two-dimensional array of electrodes, (2) achieving controlled dielectric droplet injection, (3) fusing and reacting droplets, and (4) demonstrating a protein fluorescence assay using micro-droplets. ^

Determining RNA solution structure by segmental isotopic labeling and NMR: application to Caenorhabditis elegans spliced leader RNA 1.

Recent developments in multidimensional heteronuclear NMR spectroscopy and large-scale synthesis of uniformly 13C- and 15N-labeled oligonucleotides have greatly improved the prospects for determination of the solution structure of RNA. However, there are circumstances in which it may be advantageous to label only a segment of the entire RNA chain. For example, in a larger RNA molecule the structural question of interest may reside in a localized domain. Labeling only the corresponding nucleotides simplifies the spectrum and resonance assignments because one can filter proton spectra for coupling to 13C and 15N. Another example is in resolving alternative secondary structure models that are indistinguishable in imino proton connectivities. Here we report a general method for enzymatic synthesis of quantities of segmentally labeled RNA molecules required for NMR spectroscopy. We use the method to distinguish definitively two competing secondary structure models for the 5' half of Caenorhabditis elegans spliced leader RNA by comparison of the two-dimensional [15N] 1H heteronuclear multiple quantum correlation spectrum of the uniformly labeled sample with that of a segmentally labeled sample. The method requires relatively small samples; solutions in the 200-300 microM concentration range, with a total of 30 nmol or approximately 40 micrograms of RNA in approximately 150 microliters, give strong NMR signals in a short accumulation time. The method can be adapted to label an internal segment of a larger RNA chain for study of localized structural problems. This definitive approach provides an alternative to the more common enzymatic and chemical footprinting methods for determination of RNA secondary structure.

(Table 1) Ratio of hydroxy-GDGT vs. the total core GDGT was calculated based on the detection of hydroxy-GDGT

Hydroxylated glycerol dialkyl glycerol tetraethers (hydroxy-GDGTs) were detected in marine sediments of diverse depositional regimes and ages. Mass spectrometric evidence, complemented by information gleaned from two-dimensional (2D) 1H-13C nuclear magnetic resonance (NMR) spectroscopy on minute quantities of target analyte isolated from marine sediment, allowed us to identify one major compound as a monohydroxy-GDGT with acyclic biphytanyl moieties (OH-GDGT-0). NMR spectroscopic and mass spectrometric data indicate the presence of a tertiary hydroxyl group suggesting the compounds are the tetraether analogues of the widespread hydroxylated archaeol derivatives that have received great attention in geochemical studies of the last two decades. Three other related compounds were assigned as acyclic dihydroxy-GDGT (2OH-GDGT-0) and monohydroxy-GDGT with one (OH-GDGT-1) and two cyclopentane rings (OH-GDGT-2). Based on the identification of hydroxy-GDGT core lipids, a group of previously reported unknown intact polar lipids (IPLs), including the ubiquitously distributed H341-GDGT (Lipp J. S. and Hinrichs K. -U. (2009) Structural diversity and fate of intact polar lipids in marine sediments. Geochim. Cosmochim. Acta 73, 6816-6833), and its analogues were tentatively identified as glycosidic hydroxy-GDGTs. In addition to marine sediments, we also detected hydroxy-GDGTs in a culture of Methanothermococcus thermolithotrophicus. Given the previous finding of the putative polar precursor H341-GDGT in the planktonic marine crenarchaeon Nitrosopumilus maritimus, these compounds are synthesized by representatives of both cren- and euryarchaeota. The ubiquitous distribution and apparent substantial abundance of hydroxy-GDGT core lipids in marine sediments (up to 8% of total isoprenoid core GDGTs) point to their potential as proxies.

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08