Desenvolupament computacional de la semblança molecular quàntica

La present Tesi Doctoral, titulada desenvolupament computacional de la semblança molecular quàntica, tracta, fonamentalment, els aspectes de càlcul de mesures de semblança basades en la comparació de funcions de densitat electrònica.El primer capítol, Semblança quàntica, és introductori. S'hi descriuen les funcions de densitat de probabilitat electrònica i llur significança en el marc de la mecànica quàntica. Se n'expliciten els aspectes essencials i les condicions matemàtiques a satisfer, cara a una millor comprensió dels models de densitat electrònica que es proposen. Hom presenta les densitats electròniques, mencionant els teoremes de Hohenberg i Kohn i esquematitzant la teoria de Bader, com magnituds fonamentals en la descripció de les molècules i en la comprensió de llurs propietats.En el capítol Models de densitats electròniques moleculars es presenten procediments computacionals originals per l'ajust de funcions densitat a models expandits en termes de gaussianes 1s centrades en els nuclis. Les restriccions físico-matemàtiques associades a les distribucions de probabilitat s'introdueixen de manera rigorosa, en el procediment anomenat Atomic Shell Approximation (ASA). Aquest procediment, implementat en el programa ASAC, parteix d'un espai funcional quasi complert, d'on se seleccionen variacionalment les funcions o capes de l'expansió, d'acord als requisits de no negativitat. La qualitat d'aquestes densitats i de les mesures de semblança derivades es verifica abastament. Aquest model ASA s'estén a representacions dinàmiques, físicament més acurades, en quant que afectades per les vibracions nuclears, cara a una exploració de l'efecte de l'esmorteïment dels pics nuclears en les mesures de semblança molecular. La comparació de les densitats dinàmiques respecte les estàtiques evidencia un reordenament en les densitats dinàmiques, d'acord al que constituiria una manifestació del Principi quàntic de Le Chatelier. El procediment ASA, explícitament consistent amb les condicions de N-representabilitat, s'aplica també a la determinació directe de densitats electròniques hidrogenoides, en un context de teoria del funcional de la densitat.El capítol Maximització global de la funció de semblança presenta algorismes originals per la determinació de la màxima sobreposició de les densitats electròniques moleculars. Les mesures de semblança molecular quàntica s'identifiquen amb el màxim solapament, de manera es mesuri la distància entre les molècules, independentment dels sistemes de referència on es defineixen les densitats electròniques. Partint de la solució global en el límit de densitats infinitament compactades en els nuclis, es proposen tres nivells de aproximació per l'exploració sistemàtica, no estocàstica, de la funció de semblança, possibilitant la identificació eficient del màxim global, així com també dels diferents màxims locals. Es proposa també una parametrització original de les integrals de recobriment a través d'ajustos a funcions lorentzianes, en quant que tècnica d'acceleració computacional. En la pràctica de les relacions estructura-activitat, aquests avenços possibiliten la implementació eficient de mesures de semblança quantitatives, i, paral·lelament, proporcionen una metodologia totalment automàtica d'alineació molecular. El capítol Semblances d'àtoms en molècules descriu un algorisme de comparació dels àtoms de Bader, o regions tridimensionals delimitades per superfícies de flux zero de la funció de densitat electrònica. El caràcter quantitatiu d'aquestes semblances possibilita la mesura rigorosa de la noció química de transferibilitat d'àtoms i grups funcionals. Les superfícies de flux zero i els algorismes d'integració usats han estat publicats recentment i constitueixen l'aproximació més acurada pel càlcul de les propietats atòmiques. Finalment, en el capítol Semblances en estructures cristal·lines hom proposa una definició original de semblança, específica per la comparació dels conceptes de suavitat o softness en la distribució de fonons associats a l'estructura cristal·lina. Aquests conceptes apareixen en estudis de superconductivitat a causa de la influència de les interaccions electró-fonó en les temperatures de transició a l'estat superconductor. En aplicar-se aquesta metodologia a l'anàlisi de sals de BEDT-TTF, s'evidencien correlacions estructurals entre sals superconductores i no superconductores, en consonància amb les hipòtesis apuntades a la literatura sobre la rellevància de determinades interaccions.Conclouen aquesta tesi un apèndix que conté el programa ASAC, implementació de l'algorisme ASA, i un capítol final amb referències bibliogràfiques.

Contribución al estudio de la extracción química del Fe3+ contaminante de la madera arqueológica subacuática impregnada con polietilenglicol

Due to the large quantity of contamination by Fe in the waterlogged wood and the composites previously processed with poliethilenglycol, PEG , we have thought the possible extraction and formation of complexes Fe-L (L= 2-Phosphonobuta-1,2,4- tricarboxylic acid, (PBTC)) and their effect on (i) structure of the wood, (ii) structure and physiques characteristics of PEG and (iii) post-treatment contamination by Fe coming from atmospheric agents. This work is a project for to study the formation of these complexes and possible modifications in structures.

Rational modification of the hierarchy of intermolecular interactions in molecular crystal structures by using tunable halogen bonds

A family of 16 isomolecular salts (3-XpyH)(2)[MX'(4)] (3-XpyH=3-halopyridinium; M=Co, Zn; X=(F), Cl, Br, (I); X'=Cl, Br, I) each containing rigid organic cations and tetrahedral halometallate anions has been prepared and characterized by X-ray single crystal and/or powder diffraction. Their crystal structures reflect the competition and cooperation between non-covalent interactions: N-H center dot center dot center dot X'-M hydrogen bonds, C-X center dot center dot center dot X'-M halogen bonds and pi-pi stacking. The latter are essentially unchanged in strength across the series, but both halogen bonds and hydrogen bonds are modified in strength upon changing the halogens involved. Changing the organic halogen (X) from F to I strengthens the C-X center dot center dot center dot X'-M halogen bonds, whereas an analogous change of the inorganic halogen (X') weakens both halogen bonds and N-H center dot center dot center dot X'-M hydrogen bonds. By so tuning the strength of the putative halogen bonds from repulsive to weak to moderately strong attractive interactions, the hierarchy of the interactions has been modified rationally leading to systematic changes in crystal packing. Three classes of crystal structure are obtained. In type A (C-F center dot center dot center dot X'-M) halogen bonds are absent. The structure is directed by N-H center dot center dot center dot X'-M hydrogen bonds and pi-stacking interactions. In type B structures, involving small organic halogens (X) and large inorganic halogens (X'), long (weak) C-X center dot center dot center dot X'-M interactions are observed with type I halogen-halogen interaction geometries (C-X center dot center dot center dot X' approximate to X center dot center dot center dot X'-M approximate to 155 degrees), but hydrogen bonds still dominate. Thus, minor but quite significant perturbations from the type A structure arise. In type C, involving larger organic halogens (X) and smaller inorganic halogens (X'), stronger halogen bonds are formed with a type II halogen-halogen interaction geometry (C-X center dot center dot center dot X' approximate to 180 degrees; X center dot center dot center dot X'-M approximate to 110 degrees) that is electrostatically attractive. The halogen bonds play a major role alongside hydrogen bonds in directing the type C structures, which as a result are quite different from type A and B.

Fe-sulphate-rich evaporative mineral precipitates from the Rio Tinto, southwest Spain

The soluble metal sulphate salts melanterite, rozenite, rhomboclase, szornolnokite, copiapite, coquimbite, hexahydrite and halotrichite, together with gypsum, have been identified, some for the first time oil the banks of the Rio Tinto, SW Spain. Secondary Fe-sulphate minerals call form directly from evaporating acid, sulphate-rich Solutions as a result of pyrite oxidation. Chemical analyses of mixtures of these salt minerals indicate concentrations of Fe (up to 31 wt.%), Mg (up to 4 wt.%), Cu (up to 2 wt.%) and Zn (up to wt.%). These minerals are shown to act as transient storage Cor metals and can store on average up to 10% (9.5 - 11%) and 22% (20-23%) Zn and Cu respectively, of the total discharge of the Rio Tinto during the summer period. Melanterite and rozenite precipitates at Rio Tinto are only found in association with very acidic drainage waters (pH <1.0) draining directly from pyritic waste piles. Copiapite precipitates abundantly oil the banks of the Rio Tinto by (1) direct evaporation of the river water; or (2) as part of a paragenetic sequence with the inclusion of minor halotrichite, indicating natural dehydration and decomposition. The natural occurrences are comparable with the process of paragenesis from the evaporation of Rio Tinto river water under laboratory experiments resulting in the formation of aluminocopiapite, halotrichite, coquimbite, voltaite and gypsum.

Impact of sewage sludge applications on the biogeochemistry of soils

This report describes an investigation into the bioavailability and fate of trace metals and their subsequent impact on important soil microbiological functions such as nitrification, denitrification and methane oxidation in low and high Cu containing soils in the presence and absence of residual organic matter from sewage sludge additions made 10 years earlier. The soils being studied are part of long term sewage sludge trials and include a low Cu soil ( 13.3mg Cu/ kg soil, 4.18 LOI %), left un- amended to serve as a control soil, soil amended with a high Cu sewage sludge ( 278.3mg Cu/ kg soil, 6.52 LOI %) and soil amended with a low Cu sewage sludge ( 46.3mg Cu/ kg soil, 6.18 LOI %). Soil was also amended with inorganic metal salts ( 273.4mg Cu/ kg soil, 4.52 LOI %) to further investigate the impact of Cu in the absence of additional organic matter contained in applied sewage sludge. Data from the first two years of a project are presented which has included field- based studies at long term sewage sludge trials based in Watlington, Oxford, UK and laboratory based studies at the Institute of Grassland & Environmental Research, North Wyke, Devon, UK.

Influence of aluminum hydroxide on potassium release from two Colombian soils

The effect of sesquioxides on the mechanisms of chemical reactions that govern the transformation between exchangeable potassium (Kex) and non-exchangeable K (Knex) was studied on acid tropical soils from Colombia: Caribia with predominantly 2 : 1 clay minerals and High Terrace with predominantly 1 : 1 clay minerals and sesquioxides. Illite and vermiculite are the main clay minerals in Caribia followed by kaolinite, gibbsite, and plagioclase, and kaolinite is the major clay mineral in High Terrace followed by hydroxyl-Al interlayered vermiculite, quartz, and pyrophyllite. The soils have 1.8 and 0.5% of K2O, respectively. They were used either untreated or prepared by adding AlCl3 and NaOH, which produced aluminum hydroxide. The soils were percolated continuously with 10mM NH4OAc at pH 7.0 and 10 mM CaCl2 at pH 5.8 for 120 h at 6 mL h(-1) to examine the release of Kex and Knex. In the untreated soils, NH4+ and Ca-2(+) released the same amounts of Kex from Caribia, whereas NH4+ released about twice as much Kex as Ca2+ from High Terrace. This study proposes that the small ionic size of NH4+ (0.54nm) enables it to enter more easily into the K sites at the broken edges of the kaolinite where Ca2+ (0.96 nm) cannot have access. As expected for a soil dominated by 2 : 1 clay minerals, Ca2+ caused Knex to be released from Caribia with no release by NH4+. No Knex was released by either ion from High Terrace. After treatment with aluminum hydroxide, K release from the exchangeable fraction was reduced in Caribia due to the blocking of the exchange sites but release of Knex was not affected. The treatment increased the amount of Kex released from the High Terrace soil and the release of Knex remained negligible although with Ca2+ the distinction between Kex and Knex was unclear. The increase in Kex was attributed to the initially acidic conditions produced by adding AlCl3 which may have dissolved interlayered aluminum hydroxide from the vermiculite present, thus exposing trapped K as exchangeable K. The subsequent precipitation of aluminum hydroxide when NaOH was added did not interfere with the release of this K, and so was probably formed mostly on the surface of the dominant kaolinite. Measurement of availability of K by standard methods using NH4 salts could result in overestimates in High Terrace and this may be a more general shortcoming of the methods in kaolinitic soils.

Hydrolysis of N2O5 on sub-micron mineral salt aerosols

The kinetics of reactive uptake of gaseous N2O5 on sub-micron aerosol particles composed of aqueous ammonium sulfate, ammonium hydrogensulfate and sodium nitrate has been investigated. Uptake was measured in a laminar flow reactor, coupled with a differential mobility analyser (DMA) to obtain the aerosol size distribution, with N2O5 detection using NO chemiluminescence. FTIR spectroscopy was used to obtain information about the composition and water content of the aerosol particles under the conditions used in the kinetic measurements. The aerosols were generated by the nebulisation of aqueous salt solutions. The uptake coefficient on the sulfate salts was in the range [gamma]=0.0015 to 0.033 depending on temperature, humidity and phase of the aerosol. On sodium nitrate aerosols the values were much lower, [gamma]<0.001, confirming the inhibition of N2O5 hydrolysis by nitrate ions. At high humidity (>50% r.h.) the uptake coefficient on liquid sulfate aerosols is independent of water content, but at lower humidity, especially below the efflorescence point, the reactivity of the aerosol declines, correlating with the lower water content. The lower uptake rate on solid aerosols may be due to limitations imposed by the liquid volume in the particles. Uptake on sulfate aerosols showed a negative temperature dependence at T>290 K but no significant temperature dependence at lower temperatures. The results are generally consistent with previous models of N2O5 hydrolysis where the reactive intermediate is NO2+ produced by autoionisation of nitrogen pentoxide in the condensed phase.

Effects of stabiliser addition and in-container sterilisation on selected properties of milk related to casein micelle stability

Different stabilising salts and calcium chloride were added to raw milk to evaluate changes in pH, ionic calcium, ethanol stability, casein micelle size and zeta potential. These milk samples were then sterilised at 121 °C for 15 min and stored for 6 months to determine how these properties changed. Addition of tri-sodium citrate (TSC) and di-sodium hydrogen phosphate (DSHP) to milk reduced ionic calcium, increased pH and increased ethanol stability in a concentration-dependent fashion. There was relatively little change in casein micelle size and a slight decrease in zeta potential. Sodium hexametaphosphate (SHMP) also reduced ionic calcium considerably, but its effect on pH was less noticeable. In contrast, sodium dihydrogen phosphate (SDHP) reduced pH but had little effect on ionic calcium. In-container sterilisation of these samples reduced pH, increased ethanol stability and increased casein micelle size, but had variable effects on ionic calcium; for DSHP and SDHP, ionic calcium decreased after sterilisation but, for SHMP, it remained little changed or increased. Milk containing 3.2 mM SHMP and more than 4.5 mM CaCl2 coagulated upon sterilisation. All other samples were stable but there were differences in browning, which increased in intensity as milk pH increased. Heat-induced sediment was not directly related to ionic calcium concentration, so reducing ionic calcium was not the only consideration in terms of improving heat stability. After 6 months of storage, the most acceptable product, in appearance, was that containing SDHP, as this minimised browning during sterilisation and further development of browning during storage.

Saturated salt solutions for humidity control and the survival of dry powder and oil formulations of Beauveria bassiana conidia

Oil-based formulated conidia sprayed on steel plates and conidia powder (control) of Beauveria bassiana isolate IMI 386243 were stored at temperatures from 10 to 40 degrees C in desiccators over saturated salt solutions providing relative humidities from 32 to 88%, or in hermetic storage at 40 degrees C, and moisture contents in equilibrium with 33 or 77% relative humidity. The negative semi-logarithmic relation (P < 0.005) between conidia longevity (at 40 degrees C) and equilibrium relative humidity did not differ (P > 0.25) between formulated conidia and conidia powder. Despite this, certain saturated salts provided consistently greater longevity (NaCl) and others consistently shorter longevity (KCl) for formulated conidia compared to conidia powder. These results, analysis of previous data, and comparison with hermetic storage, indicate that storage of conidia over saturated salt solutions provides inconsistent responses to environment and so may be problematic for bio-pesticide research. In hermetic storage, oil formulation was not deleterious to longevity and in the more moist environment enhanced survival periods. (c) 2005 Elsevier Inc. All rights reserved.

A review and simplification of the in vitro incubation medium

The requirement to rapidly and efficiently evaluate ruminant feedstuffs places increased emphasis on in vitro systems. However, despite the developmental work undertaken and widespread application of such techniques, little attention has been paid to the incubation medium. Considerable research using in vitro systems is conducted in resource-poor developing countries that often have difficulties associated with technical expertise, sourcing chemicals and/or funding to cover analytical and equipment costs. Such limitations have, to date, restricted vital feed evaluation programmes in these regions. This paper examines the function and relevance of the buffer, nutrient, and reducing solution components within current in vitro media, with the aim of identifying where simplification can be achieved. The review, supported by experimental work, identified no requirement to change the carbonate or phosphate salts, which comprise the main buffer components. The inclusion of microminerals provided few additional nutrients over that already supplied by the rumen fluid and substrate, and so may be omitted. Nitrogen associated with the inoculum was insufficient to support degradation and a level of 25 mg N/g substrate is recommended. A sulphur inclusion level of 4-5 mg S/g substrate is proposed, with S levels lowered through omission of sodium sulphide and replacement of magnesium sulphate with magnesium chloride. It was confirmed that a highly reduced medium was not required, provided that anaerobic conditions were rapidly established. This allows sodium sulphide, part of the reducing solution, to be omitted. Further, as gassing with CO2 directly influences the quantity of gas released, it is recommended that minimum CO, levels be used and that gas flow and duration, together with the volume of medium treated, are detailed in experimental procedures. It is considered that these simplifications will improve safety and reduce costs and problems associated with sourcing components, while maintaining analytical precision. (c) 2005 Elsevier B.V. All rights reserved.

Concentration of aluminium in breast cyst fluids collected from women affected by gross cystic breast disease

Gross cystic breast disease (GCBD) is the most common benign breast disorder, but the molecular basis of cyst formation remains to be identified. If the use of aluminium-based antiperspirant salts is involved in the etiology of gross breast cyst formation, it might be expected that aluminium would be at elevated levels in human breast cyst fluid (BCF). Aluminium was measured by ICP-MS in 48 samples of BCF, 30 samples of human blood serum and 45 samples of human breast milk at different stages of lactation (colostrum, intermediate, mature). The median level of aluminium in apocrine type I BCF (n:= 27, 150 mu g I-1) was significantly higher than in transuclative type II BCF (n = 21, 32 mu g I-1; P < 0.0001). By comparison, aluminium measurements gave a median concentration of 6 mu g I-1 in human serum and 25 mu g I-1 in human breast milk, with no difference between colostrum, intermediate and mature milk. Levels of aluminium were significantly higher in both types of BCF than in human serum (P < 0.0001). However when compared with human breast milk, aluminium levels were only significantly higher in apocrine type I BCF (P < 0.0001) and not in transudative type II BCF (P = 0.152). It remains to be identified why such high levels of aluminium were found in the apocrine type I BCF and from where the aluminium originated. However, if aluminium-based antiperspirants are found to be the source and to play any causal role in development of breast cysts, then it might become possible to prevent this common breast disorder. Copyright (C) 2008 John Wiley & Sons, Ltd.

Aluminium, antiperspirants and breast cancer

Aluminium salts are used as the active antiperspirant agent in underarm cosmetics, but the effects of widespread, long term and increasing use remain unknown, especially in relation to the breast, which is a local area of application. Clinical studies showing a disproportionately high incidence of breast cancer in the upper outer quadrant of the breast together with reports of genomic instability in outer quadrants of the breast provide supporting evidence for a role for locally applied cosmetic chemicals in the development of breast cancer. Aluminium is known to have a genotoxic profile, capable of causing both DNA alterations and epigenetic effects, and this would be consistent with a potential role in breast cancer if such effects occurred in breast cells. Oestrogen is a well established influence in breast cancer and its action, dependent on intracellular receptors which function as ligand-activated zinc finger transcription factors, suggests one possible point of interference from aluminium. Results reported here demonstrate that aluminium in the form of aluminium chloride or aluminium chlorhydrate can interfere with the function of oestrogen receptors of MCF7 human breast cancer cells both in terms of ligand binding and in terms of oestrogen-regulated reporter gene expression. This adds aluminium to the increasing list of metals capable of interfering with oestrogen action and termed metal I oestrogens. Further studies are now needed to identify the molecular basis of this action, the longer term effects of aluminium exposure and whether aluminium can cause aberrations to other signalling pathways in breast cells. Given the wide exposure of the human population to antiperspirants, it will be important to establish dermal absorption in the local area of the breast and whether long term low level absorption could play a role in the increasing incidence of breast cancer. (c) 2005 Elsevier Inc. All rights reserved.