Solubility prediction usually refers to prediction of the intrinsic aqueous solubility, which is the concentration of an unionised molecule in a saturated aqueous solution at thermodynamic equilibrium at a given temperature. Solubility is determined by structural and energetic components emanating from solid-phase structure and packing interactions, solute–solvent interactions, and structural reorganisation in solution. An overview of the most commonly used methods for solubility prediction is given in Chapter 1. In this thesis, we investigate various approaches to solubility prediction and solvation model development, based on informatics and incorporation of empirical and experimental data. These are of a knowledge-based nature, and specifically incorporate information from the Cambridge Structural Database (CSD). A common problem for solubility prediction is the computational cost associated with accurate models. This issue is usually addressed by use of machine learning and regression models, such as the General Solubility Equation (GSE). These types of models are investigated and discussed in Chapter 3, where we evaluate the reliability of the GSE for a set of structures covering a large area of chemical space. We find that molecular descriptors relating to specific atom or functional group counts in the solute molecule almost always appear in improved regression models. In accordance with the findings of Chapter 3, in Chapter 4 we investigate whether radial distribution functions (RDFs) calculated for atoms (defined according to their immediate chemical environment) with water from organic hydrate crystal structures may give a good indication of interactions applicable to the solution phase, and justify this by comparison of our own RDFs to neutron diffraction data for water and ice. We then apply our RDFs to the theory of the Reference Interaction Site Model (RISM) in Chapter 5, and produce novel models for the calculation of Hydration Free Energies (HFEs).

In the studies underlying this thesis, various source tracing techniques were applied to environmental samples from the Baltic region. Comprehensive sampling and analysis of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) in surface sediments in Swedish coastal and offshore areas resulted in a unique data set for this region. Nearly 150 samples of surface sediments were analyzed for all tetra- to octa-chlorinated PCDD/Fs. The levels showed large spatial variability with hotspots in several coastal regions. Neither Sweden nor the EU has introduced guideline values for PCDD/Fs in sediment, but comparisons to available guidelines and quality standards from other countries indicate that large areas of primarily coastal sediments may constitute a risk to marine organisms. Multivariate pattern analysis techniques and receptor models, such as Principal Component Analysis (PCA) and Positive Matrix Factorization (PMF), were used to trace sources. These analyses suggested that three to six source types can explain most of the observed pattern variations found in the sediment samples. Atmospheric deposition was suggested as the most important source to offshore areas, thus confirming earlier estimates. However, spatial differences indicated a larger fraction of local/regional atmospheric sources, characterized by PCDFs, in the south. This was indicated by the identification of several patterns of atmospheric origin. In coastal areas, the influence of direct emission sources was larger, and among these, chlorophenol used for wood preservation and emissions from pulp/paper production and other wood related industry appeared to be most important. The historic emissions connected to processes involving chemical reactions with chlorine (e.g. pulp bleaching) were found to be of less importance except at some coastal sites. The analysis of PCDD/Fs in Baltic herring also revealed spatial variations in the levels and pollution patterns along the coast. The geographical match against areas with elevated sediment levels indicated that transfer from sediments via water to organisms was one possible explanation. Fugacity, a concept used to predict the net transport direction between environmental matrices, was used to explore the gas exchange of hexachlorocyclohexanes (HCHs) and polychlorinated biphenyls (PCBs) between air and water. These estimates suggested that, in the Kattegat Sea, the gaseous exchange of HCHs primarily resulted in net deposition while PCBs were net volatilized under certain environmental conditions. The study also indicated that, while the air concentrations of both PCBs and γ-HCH are mostly dependent upon the origin of the air mass, the fluctuations in α-HCH were primarily influenced by seasonal changes.

El càncer de pàncrees és altament agressiu i representa la cinquena causa de mort al mon occidental. Anteriorment, en el nostre laboratori, vam identificar que el receptor tissular del plasminogen (tPA) hi està sobre-expressat i juga un paper important el la progressió tumoral. En la present tesi hem profunditzat en l'estudi del mecanisme molecular de tPA i seus receptors en aquest càncer. En primer lloc hem caracteritzat en detall la interacció de tPA amb Annexina A2 (principal receptor de tPA en endoteli i altament expressada en pàncrees) demostrant que les dades publicades sobre la seqüència responsable de la interacció no eren correctes. A més a més hem caracteritzat les proteïnes de lisats cel·lulars pancreàtics que interaccionen amb tPA mitjançant un assaig pull down i posterior anàlisi proteòmic. de tot identificant un conjunt de possibles lligands de tPA. D'entre aquests hem seleccionat galectina 1, una lectina que mai s'ha descrit que interaccioni amb tPA, per realitzar la caracterització bioquímica i funcional del seu paper com a nou lligand de tPA en càncer de pàncrees. / Pancreatic cancer is a highly aggressive disease and represents the fifth cause of death in occidental world. Our laboratory has previously reported tissue type plasminogen activator (tPA) over expression in this cancer and its role in tumoral progression. During the present thesis we have studied tPA and its molecular mechanism through its receptors in this tumor.We have first characterized tPA interaction with annexin A2 (its main receptor in endothelium and highly expressed in pancreas). Our results showed that published data about the sequence responsible of this interaction was not correct. We have also identified a set of new putative tPA receptors in pancreatic cell lisates using a pull down assay and proteomic analysis. One of the proteins identified was galectin 1, a lectin with not know relation with tPA. We performed a biochemical and functional characterization of the interaction between these two proteins in pancreatic cancer.

Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechanics, molecular dynamics and ab initio techniques. Simulated quartz surfaces covered the range of surface charge densities 0.00, -0.03, -0.06 and -0.12 C-m-2, approximately corresponding to pH values 4.5, 7.5, 9.5 and 11. As model molecules, benzoic acid, phenol, o-salicylic acid and their conjugated bases were chosen. My task was to prepare topologies and parametric models of selected organic matter basic building blocks organic molecules. I focused on studying interactions of these molecules in an aqueous environment with mineral surface quartz. The aim was to process simulation results and analyse conformations of the adsorption complexes and their thermodynamic properties such as interaction energies, free energies and adsorption geometries.

High levels of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) in edible fish in the Baltic Sea have raised health concerns in the Baltic region and the rest of Europe. Thus, there are urgent needs to characterize sources in order to formulate effective mitigation strategies. The aim of this thesis is to contribute to a better understanding of past and present sources of PCDD/Fs in the Baltic Sea environment by exploring chemical fingerprints in sediments, air, and biota. The spatial and temporal patterns of PCDD/F distributions in the Baltic Sea during the 20th century were studied in Swedish coastal and offshore sediment cores. The results showed that PCDD/F levels peaked in 1975 (± 7 years) in coastal and 1991 (± 5 years) in offshore areas. The time trends of PCDD/Fs in the sediment cores also showed that environmental half-lives of these pollutants have been shorter in coastal than in offshore areas (15 ± 5 and 29 ± 14 years, respectively). Consequently, there have been remarkable recoveries in coastal areas, but slower recovery in offshore areas with 81 ± 12% and 38 ± 11% reductions from peak levels, respectively. Source-to-receptor multivariate modeling by Positive Matrix Factorization (PMF) showed that six types of PCDD/F sources are and have been important for the Baltic Sea environment: PCDD/Fs related to i) atmospheric background, ii) thermal processes, iii) manufacture and use of tetra-chlorophenol (TCP) and iv) penta-chlorophenol (PCP), v) industrial use of elementary chlo- rine and the chloralkali-process (Chl), and vi) hexa-CDD sources. The results showed that diffuse sources (i and ii) have consistently contributed >80% of the total amounts in the Southern Baltic Sea. In the Northern Baltic Sea, where the biota is most heavily contaminated, impacts of local sources (TCP, PCP and Chl) have been higher, contributing ca. 50% of total amounts. Among the six sources, only Thermal and chlorophenols (ii-iv) have had major impacts on biota. The impact of thermal sources has, however, been declining as shown from source apportioned time-trend data of PCDD/Fs in Baltic herring. In contrast, impacts of chlorophenol-associated sources generally increased, remained at steady-state or slowly decreased during 1990-2010, suggesting that these sources have substantially contributed to the persistently high levels of PCDD/Fs in Baltic biota. Atmospheric sources of PCDD/Fs for the Baltic region (Northern Europe) were also investigated, and specifically whether the inclusion of parallel measurements of metals in the analysis of air would help back-tracking sources. PCDD/Fs and metals in high-volume air samples from a rural field station near the shore of the central Baltic Sea were measured. The study focused on the winter season and air from the S and E sectors, as these samples showed elevated levels of PCDD/Fs, particularly PCDFs. Several metals were found to correlate significantly with the PCDFs. The wide range of candidate metals as source markers for PCDD/F emissions, and the lack of an up-to-date extensive compilation of source characteristics for metal emission from vari- ous sources, limited the use of the metals as source markers. The study was not able to pin-point primary PCDD/F sources for Baltic air, but it demonstrated a new promising approach for source tracing of air emissions. The best leads for back-tracking primary sources of atmospheric PCDD/Fs in Baltic air were seasonal trends and PCDD/F congener patterns, pointing at non-industrial related thermal sources related to heating. The non-localized natures of the sources raise challenges for managing the emissions and thus societal efforts are required to better control atmospheric emissions of PCDD/Fs. / EcoChange / BalticPOPs