Tesis Doctorals - Facultat - Química

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Development of a framework for data management, harmonisation, visualisation, and analytics of multi-omics clinical trials data in the context of autoimmune diseases
(Universitat de Barcelona, 2025-12-19) Leist, Ivo Christopher; Gut, Ivo Glynne; Universitat de Barcelona. Facultat de Química
[eng] (Multi-)omics technologies generate vast amounts of data that require proper organisation and storage for efficient analyses and interoperability. Historically research organisations managed data locally, but in today’s large-scale international collaborative projects, this hinders efficient data exchange. A case in point, is the use of SFTP file server for data sharing purposes, which requires familiarity with specific software or command-line tools. Commercial cloud storage (e.g., Dropbox or Google Cloud) offers an alternative but demands trust in black-box solutions and their providers. Open-source alternatives exist, each with specific strengths and limitations. In this thesis, I evaluated the applicability of these existing open-source data warehouse solutions for the 3TR project (3tr-imi.eu). It is a public-private partnership tackling seven immune-mediated diseases across 15 European countries involving 69 partners. As none of the tested software solutions met the needs of the 3TR project consortium I developed OmicsDM, a web-based platform that facilitates data storage, sharing, visualisation, and analysis. In 3TR, diseases are analysed both independently and jointly. Regarding the latter, the heterogeneity of the pheno-clinical data across studies poses a major challenge. To address this, I participated in the development of Convert-Pheno, a software toolkit for the interconversion of common data models for phenotypic data. Thus, laying the foundation for the envisioned cross-disease analysis. Next, the consortium needed a method to group patients by phenotypic resemblance rather than diagnostic labels alone. Thus, enabling researchers to construct phenotype-based cohorts whose analysis can reveal shared mechanisms or treatment responses across diseases To aid in the grouping we built Pheno-Ranker. It leverages semantic similarity to compare phenotypic data stored in GA4GH standards and beyond. For both Convert-Pheno and Pheno-Ranker I built intuitive web user interfaces, each with its own public playground to let users explore the capabilities of each of the tools. To sum it up, the developments in this thesis are an important contribution to the improvement of the biomedical data management, harmonisation, visualisation and analytics infrastructure in Europe and beyond.
Advanced synthetic strategies to control pharmacological action using ultraviolet, visible, and infrared light
(Universitat de Barcelona, 2025-12-17) Santini, Ramona; Gorostiza Langa, Pablo Ignacio; Universitat de Barcelona. Facultat de Química
[eng] Photopharmacology fuses the best features of various neuromodulation techniques, allowing high spatial and temporal control to overcome the adverse effects of systemic pharmacology. The control of neuronal activity with photopharmacology can be achieved by (1) freely diffusible ligands that exert different pharmacological actions in the dark and with light, (2) photoswitchable molecules covalently bound to their receptors that allow a more selective action, with high precision and control of a specific neuronal population, and (3) the release of active ligands by light-controlled drug encapsulation systems. In this thesis, we have used these three design strategies to neuromodulate different targets. In the first part, we have focused on photopharmacology based on ultraviolet and visible light. First, we have developed photochromic glycine receptor ligand analogues to expand the active molecules available for this class of orphan receptors, study glycinergic transmission and potentially inhibit neuropathic pain with light. We have also used ultraviolet light to trigger the selective release of glutamatergic and muscarinic ligands from supramolecular polymer-based drug encapsulation systems. We have designed two different strategies to encapsulate drugs. With the former, we have obtained good molecular coupling results using transmission electron microscopy and circular dichroism, but we have not been able to verify its efficacy in biological systems due to the low solubility of the polymer. We have overcome this barrier in the second strategy, introducing a potent muscarinic agonist into the supramolecular structure and demonstrating its release using the calcium imaging technique. In this way, we have demonstrated the applicability of this class of supramolecular polymers as selective light-activated drug delivery systems. Despite the great technical advances achieved over the last twenty years, the translation of photopharmacology to the clinic remains difficult, partly due to the toxicity and low tissue penetration of ultraviolet light. For this reason, in the second part of this thesis, we have developed photopharmacological ligands that allow the application of light more deeply and safely. First, we used two-photon excitation to control neuronal activation by means of a novel photoswitchable ligand that can covalently conjugate to native ionotropic glutamate receptors, without requiring mutagenesis. In addition, this new ligand has shown selectivity for specific subtypes of ionotropic glutamate receptors, AMPA and kainate receptors. Activation with near-infrared light by multiphoton stimulation also offers focused stimulation at the micrometer scale and in three dimensions. However, the technical complexity of multiphotonic stimulation limits its clinical applications to practice. Therefore, we have also developed photochromic ligands based on donor and acceptor Stenhouse adductes that can be photoactivated in the therapeutic window of the spectrum by excitation of a photon. These new ligands contain active barbiturates at gamma-aminobutyric acid receptors and chemical substitutions that push their absorption at infrared wavelengths. We have also studied their isomerization mechanisms to understand how to make them compatible with protic environments. The most promising compound in the library has good solubility, absorption wavelength in dark red, and antagonist activity at gamma-aminobutyric acid receptors.
Volatile Organic Compounds in the Planetary Boundary Layer: Sources, Accumulation and Vertical Distribution
(Universitat de Barcelona, 2025-12-10) Díez Palet, Isabel; Fernandez Ramón, Pilar; Grimalt Obrador, Joan; Universitat de Barcelona. Facultat de Química
[eng] Volatile organic compounds (VOCs) are emitted from a wide range of sources, and their accumulation, dispersion, and photo-oxidation are strongly influenced by meteorological conditions and boundary-layer dynamics. Some VOCs are recognized as carcinogens (e.g., benzene), others are neurotoxic (e.g., toluene), and many act as precursors of tropospheric ozone and secondary organic aerosol (SOA). Despite their importance, the vertical distribution and transformation of VOCs in the lower troposphere remain insufficiently characterized. This dissertation investigated the origins, composition, distribution, and transformation of VOCs across rural, suburban, and industrial environments in the Western Mediterranean. VOCs were collected through active offline sampling using a variety of sorbent cartridges and subsequently analyzed using GC-MS and HPLC techniques. In order to capture vertical distributions, ground-level observations were combined with vertical profiles up to 400 m using tethered balloons. This approach allowed sampling of VOCs both below and above the nocturnal residual layer. The results showed that anthropogenic activities were the dominant drivers of VOC variability, with meteorology and seasonality exerting significant secondary influences. In summer, high temperatures enhanced both biogenic emissions (e.g., isoprene) and evaporation of anthropogenic VOCs, whereas in winter shallow boundary layers favored the accumulation of traffic- and biomass-related VOCs near the surface. Source apportionment identified seven major contributors at ground-level: industrial emissions, traffic, biomass burning, temperature-dependent isoprene, gasoline evaporation, agricultural pesticides, and diesel. Their relative importance varied across sites and seasons, with industrial solvents prevailing in industrial areas, traffic and biomass in suburban sites, and agricultural emissions in rural regions. Importantly, the study revealed that a small set of anthropogenic VOCs controls oxidative capacity, ozone formation, and SOA production, with biogenic contributions becoming more relevant in summer. Vertical profiles revealed that surface sources influenced VOC composition up to 350 m AGL, with balloon height samples reflecting ground-level sources and aged compositions. A general decrease in VOC concentrations with altitude was observed due to dilution and oxidation. Primary VOCs declined by ~32% at balloon altitude and secondary VOCs showed a smaller decrease (~20%) with some carbonyl species showing a homogeneous distribution with height. Temperature inversions caused primary VOCs to accumulate near the surface, while secondary VOCs and long-lived halogenated compounds showed much lower accumulation, and some oxygenated species even exhibited higher concentrations aloft Ratios of compounds emitted from similar sources but with different reactivities (e.g., benzene/toluene) and secondary compounds to its precursors (e.g., SOA tracers/isoprene) proved effective indicators of atmospheric ageing. Aged VOCs predominated aloft across all sites, whereas ground-level air reflected stronger contributions from fresh emissions. Aloft, air masses were systematically more oxidized than near the surface, particularly in winter and in the nocturnal residual layer, and showed greater accumulation of long-lived VOCs and secondary products, including SOA. Local processes, including emission, oxidation, and boundary-layer dynamics contributed significantly to aged VOCs at higher altitudes. In particular, it was observed that, under standard conditions, the photooxidation of locally emitted compounds can contribute up to 41% to aged VOCs aloft, which may then influence the oxidative state of the residual layer once is developed. Overall, this PhD thesis advances understanding of VOC behavior in the lower troposphere by combining surface and vertical observations with robust analytical and statistical tools. The findings presented in this dissertation highlight the importance of accounting for vertical pollutant distributions and boundary-layer dynamics in atmospheric models and provide valuable insights for developing effective air quality policies in Mediterranean environments.
Aerosol emissions from wildfires and prescribed burns: implications for firefighter exposure and air quality
(Universitat de Barcelona, 2025-12-02) Gili i Ciurana, Jordina; Viana Rodríguez, María del Mar; van Drooge, Barend L.; Universitat de Barcelona. Facultat de Química
[eng] Wildland fires, including both wildfires and prescribed burns, are becoming increasingly frequent and intense across Southern Europe due to climate and land-use changes, posing growing threats to air quality and human health. However, estimating health impacts of aerosols emitted by wildfires remains a challenge, partly due to uncertainties in wildfire emissions and exposure assessment. Understanding pollutant concentrations in smoke-filled environments is key to developing mitigation strategies that protect exposed populations, public health and the environment. This doctoral thesis aims to assess the impacts of smoke emissions on ambient air and firefighters’ personal exposure to fine particulate matter (PM2.5), black carbon (BC) and polycyclic aromatic hydrocarbons (PAHs). Between 2022 and 2024, experimental field campaigns were conducted in two of Spain’s most fire-prone areas: Galicia (NW Spain) and Catalonia (NE Spain), using a combination of fixed monitors and portable sampling devices. - Air quality monitoring focused on ambient PM2.5 concentrations in Galicia using a network of PurpleAir monitors strategically deployed at firefighter stations during summer seasons over three consecutive years. Data from the 2022 campaign, marked by the highest number of large wildfires (>500 ha), was analyzed applying source apportionment tools to quantify wildfire impacts. - Personal exposure monitoring took place in Catalonia during prescribed burns and wildfires, using portable real-time PM2.5 and BC monitors (AirBeam2 and Micro-aethalometers AE51 and MA200) worn by firefighters. PAHs were analyzed in PM2.5 filters collected from BC monitors. Additionally, PAHs were determined in silicone wristbands (SWBs) worn by firefighters as passive air samplers, and air concentrations were calculated using a compound-specific kinetic uptake model. Different methods of source apportionment were applied based on the types of datasets generated: - For spatially resolved ambient PM2.5 concentrations, quasi-empirical orthogonal functions (QEOFs) obtained with Positive Matrix Factorization (PMF) were used in combination with HYSPLIT back-trajectory and Concentration Weighted Trajectory (CWT) analyses. Results from the QEOF-PMF analysis identified 18 wildfire events, with the Folgoso do Courel fire as a dominant source of PM2.5 spikes (>300 μg/m3; 1-hour mean), and also revealed transboundary smoke transport from Portugal. Personal exposure data showed significant and comparable PM2.5 and BC concentrations during wildfires and prescribed burns (wildfire mean PM2.5 = 152 μg/m3 vs. 110–145 μg/m3 for prescribed burns). BC/PM2.5 ratios indicated varying contributions of mineral aerosols to the emissions mix originating from firefighting tasks. Among these, mop-up tasks were identified as a significant contributor to PM2.5 exposures, with PM2.5 peak concentrations reaching up to 1190 μg/m3 (1-minute average). - For personal BC exposure concentrations, multi-wavelength BC data and individual PAH profiles were used to determine task-specific and source-specific contributions. Source apportionment of BC data distinguished task-specific exposure profiles: line operators (managing fire perimeters) were primarily exposed to biomass-burning BC (𝐵𝐶𝑏𝑏 = 61%), while torchers (initiating fires using fossil-fuel drip torches) were predominantly exposed to fossil-fuel BC (𝐵𝐶𝑓𝑓 = 77%). In addition, PAH analysis from filters and SWBs confirmed these task-specific exposure patterns. Torchers experienced the highest toxic burdens (mean ΣPAHs = 394 ng/m³, benzo[a]pyrene (BaP) = 56 ng/m³ on filters; ΣPAHs = 5004 ng/m³, BaP = 29 ng/m³ in SWBs), exceeding excess lifetime cancer risk (ELCR) thresholds. In contrast, liners showed lower exposures (mean ΣPAHs = 115 ng/m³, BaP = 12 ng/m³ on filters; ΣPAHs = 1642 ng/m³, BaP = 5 ng/m³ in SWBs. In addition, diagnostic isomer ratios (e.g., benzo[a]pyrene/benzo[e]pyrene indicated the relative distance from fresh emissions, while the presence of retene pointed to pine wood combustion. Overall, the integration of fixed-site ambient and portable personal real-time monitoring with passive sampling offered complementary insights into wildfire smoke exposure. The combination of these tools proved effective in identifying spatial and task-specific pollutant patterns, and was considered a valuable tool for exposure assessment. Furthermore, these methods may also contribute to the validation of smoke dispersion model and the development of mitigation strategies addressing environmental and health concerns related to wildland fires.
Exploring the human tRNAome: From transcriptional and processing dynamics to genomic organization and somatic mutagenesis
(Universitat de Barcelona, 2025-11-14) Murillo Recio, Marina; Ribas de Pouplana, Lluís; Torres, Adrian Gabriel; Universitat de Barcelona. Facultat de Química
[eng] Transfer RNAs (tRNAs) play a fundamental role in protein synthesis. They mediate the decoding of messenger RNA into specific amino acids through codon-anticodon interactions, according to the genetic code. The cellular tRNA pool is mainly determined by the transcription rate of tRNA genes (tDNAs), which is governed by many regulatory layers. Besides being transcribed, to be fully active, tRNAs undergo several post-transcriptional processing steps that include the addition of chemical modifications. Alterations in any of those steps have been implicated in diseases such as cancer and neurological disorders. Nevertheless, due to the complexity of tRNA biology, characterizing the cellular tRNA pool is quite complex and is often accompanied by methodological challenges. Therefore, many aspects of tRNA biology remain unknown and require further research to understand their full impact on diseases. For this reason, in this thesis, we focus on the application and development of bioinformatic strategies to decipher different aspects of tRNA biology. Currently, one of the most used techniques for analyzing the tRNA pool is small RNA sequencing (tRNA-Seq). However, the analysis of tRNA-Seq data requires the adaptation of the computational workflow from standard approaches. For this reason, we first developed tRNAstudio, an integrative pipeline that includes a mapping strategy that allows the characterization of tRNA processing and modification landscape, as well as the implementation of tRNA differential expression analysis. All pipeline components were integrated into a graphical user interface (GUI) that eases the analysis of tRNA-Seq data for non-computational users. Next, we focused on the functional relevance of the modification of adenine (A) to inosine (I) at position 34 of tRNA anticodons (I34-tRNAs), a modification crucial for the expansion of the decoding capacity of tRNAs. In Eukarya, this modification is catalyzed by Adenosine Deaminase Acting on tRNA (ADAT), composed of ADAT2 and ADAT3. Mutations in genes encoding ADAT have been associated with neurological disorders. To comprehend the impact of changes in the levels of I34-tRNAs, a knockdown model of ADAT2 (KD) was generated by our group. Using tRNAstudio, we analyzed the impact of ADAT2 KD on the tRNA pool. The results validated the model by verifying a reduction of I34-tRNAs in the context of ADAT2 KD. Moreover, we observed that the cell is unable to compensate for its loss by upregulating the expression of alternative tRNAs, highlighting the critical role of I34-tRNAs. Lastly, given that many factors can regulate tDNA transcription and that tDNAs are not randomly distributed within the genome, we wanted to assess whether their organization within the genome may impact their transcriptional activity. To investigate this, we first characterized the localization of tDNAs in the latest human genome assembly (T2T-CHM13), identifying patterns of tDNA clustering. We then determined that these clusters are associated with increased transcriptional activity. Building on these findings, we explored whether the transcriptional activity of tDNAs also influences their susceptibility to somatic mutagenesis. Our analysis revealed that tDNAs are exceptionally prone to accumulate somatic mutations, with mutation rates up to nine-fold higher than those of protein-coding genes. Moreover, mutation rate at tDNAs increased with transcriptional activity, and mutational loads were tumor-type and age-dependent. The analysis of mutational signatures identified APOBEC3 activity as the main contributor to tDNA somatic mutagenesis. Notably, Mutations at structurally conserved tRNA positions appear to be under negative selection, preventing mutation accumulation at these critical sites. By contrast, other positions were hypermutated, which could disrupt tRNA biogenesis and impair tRNA function, potentially contributing to cellular dysfunction. We propose that the accumulation of somatic mutagenesis at tDNAs could cause proteome heterogeneity and compromise proteostasis, factors that could contribute both to tissue aging and to the development or progression of cancer.
Exposure and Health Effects of Microplastics in Humans
(Universitat de Barcelona, 2025-10-29) Zuri, Giuseppina; Lacorte i Bruguera, Sílvia; Karanasiou, Angeliki; Universitat de Barcelona. Facultat de Química
[eng] Microplastic (MP) refers to plastic particles having diameter of 5 mm along their longest dimension. In the last decade, extensive research efforts have taken to identify and quantify MP in different environmental compartments and recently also in human samples as blood, urine, stool, lung, and placentae tissue proving human intake of MP. Because of our exposure to MP via inhalation and ingestion, this Thesis focuses in applying different analytical methods, both spectroscopic and thermal, to identify and quantify MP in air as well as bottled water to carry out a human exposure assessment through these pathways of exposure. Moreover, a migration study was done to assess the potential release of MP from face masks into water after potential incorrect waste disposal, finding that PP, PA, PES, and cellulose fibres shred from the masks. Air samples were collected both indoors from private and public settings, and outdoors using active sampling for 3 hours until 1.8 m3 of air were filtered and the particles were analysed with micro-Fourier Transform Infrared (μ-FTIR) spectroscopy to identify the presence of plastic polymers and to assess any potential differences in the concentration of MP between the areas considered and their potential sources. The areas considered were a urban area (Barcelona, Spain) and a rural area (Sassari, Italy). Indoor air samples (n=10) were collected from private houses, whilst outdoor air samples (n=11) were collected during rush hours in the main roads. Results reveal that indoor levels were higher in Sassari, while outdoor concentrations were greater in Barcelona. In Barcelona, MP comprised 2-15% indoors and 0-20% outdoors of the total particulate count (TPC), while Sassari showed 0-10% indoors and 8-18% outdoors. The predominant indoor polymers were polyacrylonitrile and nylon 6,6, used as fiber in clothing, home furnishing, while outdoor samples included PAN, nylon 6,6, and various polyethylene copolymers all used in clothing as well as automobile industry. The same technique was applied to assess the potential release of MP from face masks (n=4) into water during a migration study to mimic their behaviour when their disposal is mismanaged, or they are directly discarded in the environment. Results showed that MP can release polypropylene, polyamide, and polyester into the aquatic environment. Despite the advantages in using μ-FTIR, the major drawback is that it is size dependent and can be used to analyse particles having diameter >20 μm. Therefore, a pyrolysis-GC/MS method was developed to overcome the size-limitation and analyse MP in air and water samples with high degree of accuracy and precision in a rapid manner. This method enabled the target analysis of the several plastic polymers including polyethylene, polypropylene, polystyrene, polycarbonate, polyvinyl chloride, nylon 6,6, polyethylene terephthalate, polymethylmethacrylate, nitrile rubber, acrylonitrile butadiene styrene. Air samples collected from public libraries (n=14) in the urban area of Barcelona showed that high-density polyethylene was the only plastic polymer present, probably released from textiles, containers, and appliances. Bottled water samples (n=40) from 5 different European countries (Spain, Italy, France, Portugal, and Greece) were also studied and it was shown that high-density polyethylene was present in 33 out of 40 samples. The presence of polyethylene can be reconducted to the mechanical abrasion of the bottle cup. An in vitro toxicological test on human hepatocellular carcinoma (HepG2) cells was performed to assess the potential hepatotoxicity of leachates from high density polyethylene using both medium and organic solvent to extract the chemicals. HepG2 cells were exposed to both extractions at concentration of 1 μg μl-1 and no toxicity was observed when using cell viability and reactive oxygen species (ROS) generation as toxicological endpoints. Moreover, literature review concerning MP exposure through air (indoors and outdoors), bottled water, soft drinks, alcoholic beverages, and food was done to estimate the total daily intake of MP for adults, children and toddler. Additionally, bibliographic research about human biomonitoring and presence of MP in different samples including blood, urine, stool, placentae and lung tissues among others is presented to highlight that the widespread of MP has led to human intake. To conclude, the Thesis served (i) to verify that face masks could represent a potential source of MP in water bodies, (ii) to develop analytical methods to identify and quantify different MP polymers in air and water samples, (iii) to apply the results to assess human exposure through inhalation and ingestion and (iv) to investigate in vitro hepatotoxicity of HDPE leachates.
Computational studies of C-C and C-S cross-coupling reactions catalyzed by copper or nickel complexes
(Universitat de Barcelona, 2025-09-16) Gómez Mudarra, Francisco Alonso; Aullón López, Gabriel; Jover Modrego, Jesús; Universitat de Barcelona. Facultat de Química
[eng] This thesis has addressed the development of sustainable and efficient catalysts through the mechanistic study and modeling of homogeneous catalytic processes. It has focused on cross-coupling reactions using alternative metals to palladium, such as copper and nickel, due to their lower cost and higher availability, aligning with environmental sustainability objectives. Computational approaches have been employed to gain insights into the fundamental steps of catalytic cycles, with particular attention to processes such as bond activation and metal-ligand interactions. These studies contribute to a better understanding of the factors that influence catalytic performance and selectivity. While certain metals are traditionally favored for their efficiency and stability, ongoing research explores more accessible and tunable alternatives. In addition, statistical, microkinetic and statistical learning studies have been employed to analyze the electronic effect of substrates with different functional groups on reagents. This has allowed predicting reactivity and optimizing combinations without extensive experimentation, accelerating the selection of ideal experimental conditions, maximizing efficiency, and reducing costs. Overall, the obtained results show that it is possible to advance towards more sustainable catalytic processes through rational catalyst design and computational tools. It has contributed to the understanding of involved reaction mechanisms and can offer practical solutions for novel catalytic processes in line with green chemistry and sustainable development.
Exploring the Ligand Chemical Space with Computational Tools and its Effect on the Electronic Structure of Spin-Crossover of Different Complexity
(Universitat de Barcelona, 2025-04-29) Navarro i Maestro, Laia; Cirera Fernández, Jordi; Ruiz Sabín, Eliseo; Universitat de Barcelona. Facultat de Química
[eng] Spin-crossover (SCO) compounds are a fascinating class of molecular systems containing first-row transition metal ions with d4 to d7 electronic configurations, capable of alternate between two electronic states that are close in energy. Originally described by Cambi and co- workers in 1931 on some tris(N,N-dialkyldithiocarbamato)iron(III) complexes, this phenomenon has since grown into a vibrant field of research due to its potential applications as sensors, molecular level based switches, nanodevices, energy storage, and self-healing materials, among others. The SCO transition is triggered by an external stimulus, commonly temperature but also pressure or electromagnetic radiation, and is accompanied by significant changes in the physical properties of the system since the spin state of the metal centre is changed, including changes in the magnetic moment, colour, or structural distortions. The temperature at which the two spin states are equally populated, is defined as the transition temperature (T1/2), and is a key parameter in the physical characterization of such systems. Research into SCO compounds has predominantly focused on d6-Fe(II) coordination complexes, with numerous examples spanning mononuclear, polynuclear, and extended systems, including coordination polymers. While these systems dominate the field, other 3d metal ions capable of exhibiting SCO behaviour remain comparatively underexplored. In this thesis, some unusual systems exhibiting SCO have been studied computationally, such as Cr(II)-based, or anionic Fe(II)-based complexes. The level of complexity has also been increased, studying dinuclear Fe(II)-based metal-organic cages (MOCs) that can undergo SCO showing different types of transitions depending on the nature of the guest molecules that the cages can encapsulate. In all cases, ligand functionalization has been studied to understand how these changes affect the transitions, with the aim of design new materials with tailored properties. Different levels of computation have been used, from density functional theory (DFT) to higher-level multireference methods, like Complete Active Space Self-Consistent Field (CASSCF)/N-Electron Valence Perturbation Theory (NEVPT2) and Ab initio Ligand Field Theory (AILFT). In this thesis also a new methodology that develops density functional theories that use multiconfigurational reference wave functions, like Multiconfiguration Pair- Density Functional Theory (MC-PDFT) was used, for a Fe(II)-based SCO system that is well described both experimentally and computationally. MC-PDFT, in principle, allows a description of static and dynamic correlation with affordable computational costs and with an accuracy comparable to multireference perturbation theory methods. The results outlined in this thesis help in understanding the versatility and unique properties of SCO systems, which continue to drive interest in their applications expanding the scope of functional materials in advanced technologies.
Exploring the complexity of nanostructured catalysts with computational chemistry methods
(Universitat de Barcelona, 2025-09-16) Castro Latorre, Pablo; Neyman, Konstantin M.; Bruix Fusté, Albert; Universitat de Barcelona. Facultat de Química
[eng] Heterogeneous catalysis relies on interactions with a material’s surface to lower the energy barrier of chemical reactions, thus increasing their rate. Enhancing catalytic performance typically involves nanoscale surface modifications designed to increase the density of active sites and tailor their geometric and electronic structures at the atomic level, thereby optimizing adsorption energies, reaction intermediates stabilization, and turnover frequencies. However, the structural complexity of nanostructured multi-component catalysts precludes their understanding and rational improvement. The work presented in this thesis studies different types of technologically relevant nanostructured ceria-based catalysts varying in shape, composition, size and dimensionality. Computational simulations are used to understand the effect of the interaction of different nanostructures with CeO2 surfaces and elucidate their physical and chemical properties. First, metallic Pt clusters supported on CeO2 are studied to address the effects of electron transfer between metal particles and reducible oxides (known as Electronic Metal Support Interactions - EMSI) on the chemical properties of a Pt8 cluster. A computational strategy is proposed and critically evaluated to systematically characterize the electron transfer process and the different possible resulting electronic states. The chemical properties of the different sites and electronic states of the supported Pt8 cluster are evaluated, revealing significant effects in calculated adsorption energies due to EMSI for various reactants and intermediates. Second, the structural and electronic properties of the interface between a 2D FeO monolayer and the CeO2(111) surface are investigated. Simulations reveal a corrugated interfacial geometry, structure, consistent with experimental observations of periodic nanostructures. The electronic structure analysis indicates the presence of multiple electronic states, exhibiting an intricate interplay between the Fe2+/Fe3+ - Ce4+/Ce3+ redox couples. These calculations also reveal the importance of dispersion interactions and oxygen adsorption in the stabilization of periodic FeOx 2D nanostructures. Finally, the chemical reactivity of an oxidized Pt6O9 cluster supported on CeO2 is investigated to rationalize the high catalytic activity of oxidized ceria-supported Pt particles towards the CO oxidation reaction below room temperature. Activation energies of CO oxidation on the Pt6O9 cluster suggest that both the oxidized cluster and gas-phase O2 are the main sources of O atoms for CO2 formation. A reaction mechanism is proposed for the reaction on the Pt6O9 cluster where the CeO2 support acts as a spectator for the described catalytic cycles. Kinetic Monte Carlo simulations show the proposed mechanism to be consistent with high catalytic activity of Pt oxide clusters below room temperature.
Computational studies of electrocatalytic reactions of interest in the C, N and O cycles
(Universitat de Barcelona, 2025-06-11) Romeo, Eleonora; Calle Vallejo, Federico; Illas i Riera, Francesc; Universitat de Barcelona. Facultat de Química
[eng] The global challenge of climate change has underscored the urgent need for sustainable energy solutions that reduce dependence on fossil fuels and mitigate harmful emissions. Electrocatalysis, which enables key reactions for energy conversion, storage, and emissions reduction, plays a critical role in this transition. From the electrochemical reduction of CO2 to the generation of clean hydrogen and the mitigation of nitrogen oxide emissions, electrocatalytic processes are at the forefront of efforts to combat climate change. However, the efficiency and scalability of these processes depend heavily on the design of effective electrocatalysts. This thesis investigates key electrocatalytic reactions within the carbon, nitrogen, and oxygen cycles using density functional theory (DFT). In fact, DFT modeling is a useful approach for uncovering reaction mechanisms, material properties, and solvent interactions, enabling the rational design and optimization of electrocatalytic materials. The study introduces correction methods to refine the activity description of electrocatalysts, emphasizing the importance of solvent–adsorbate interactions and adsorbate- phase error corrections for more accurate simulations. These advancements enable better alignment between computational predictions and experimental results. The thesis also inspects specific catalytic reactions, including the oxygen evolution reaction (OER), acetylene reduction to 1,3-butadiene, and NO hydrogenation. A statistical criterion based on electrochemical symmetry is presented to identify effective OER catalysts. The beneficial influence of catalyst morphology, surface composition, and co-adsorbed anions on acetylene reduction is explored. In the case of NO hydrogenation, the use of catalytic matrices allowed for a deeper understanding of structural sensitivity and selectivity trends across various transition metal electrodes. The comparison of the computational hydrogen electrode (CHE) and the Grand Canonical DFT (GC-DFT) models demonstrates the advantages of GC-DFT in providing a more detailed and accurate description of catalytic behavior under applied potentials.
Comprehensive characterization of anthropogenic impacts on Mediterranean intermittent streams using cheminformatics and environmental risk assessment approaches
(Universitat de Barcelona, 2025-07-25) Gómez Navarro, Olga; Pérez, Sandra; Montemurro, Nicola; Universitat de Barcelona. Facultat de Química
[eng] Intermittent streams, characterized by variable and discontinuous flow regimes, are becoming increasingly common in the Mediterranean region due to climate change, population growth and land use changes, which further decrease water availability. As a result, the natural dilution capacity of streams is limited, making them highly vulnerable to both anthropogenic pressures and climate-driven hydrological variability. Among the key stressors, wastewater treatment plants (WWTPs) are one of the major sources of contaminants of emerging concern (CECs) and their transformation products (TPs). These are continuously being released into the environment and their detection in surface water can pose significant environmental risk due to their persistence, bioactivity, and incomplete removal during wastewater treatment. In this context, this thesis aimed to develop and apply robust analytical techniques for the detection, quantification and characterization of CECs and TPs, as well as to assess their potential environmental risks in Mediterranean freshwater systems, including both surface and groundwater, with a particular focus on under- studied regions as the Middle East North African (MENA) region. An analytical method based on solid phase extraction combined with liquid chromatography coupled to high resolution mass spectrometry was developed and validated for the detection and quantification of 116 CECs. The method demonstrated high sensitivity and broad applicability in both surface and groundwater samples. It was applied for the analysis of samples collected across multiple locations in Southern European countries (Spain, Italy, France) and MENA countries (Algeria, Tunisia), enabling a comparative assessment of water quality between northern and southern Mediterranean regions. Special attention was given to MENA countries, where comprehensive monitoring efforts have been previously lacking. Through an integrated approach combining chemical, ecological, and hydrological indicators, the study highlighted the cumulative impact of wastewater discharges on aquatic ecosystems and emphasized the need for region-specific monitoring frameworks. The importance of considering hydrological variability, particularly in low flow conditions, where natural dilution capacities of streams are limited was also emphasized, especially as water scarcity increases. The correlations between various indicators were assessed where CECs concentrations and benthic indices (ecological) revealed a moderate positive relationship. Environmental risk assessments were conducted by calculating risk quotients to evaluate the potential ecological impact associated to the detected concentrations. This approach enabled the identification of several priority pollutants, including diclofenac, losartan and azithromycin, which were consistently found in surface water at ecologically relevant concentrations, posing potential environmental risks across the five Mediterranean countries studied. In Tunisian groundwater, compounds including azithromycin, ibuprofen and caffeine were also detected at concentration levels indicating potential ecological risks. Notably the overlap in potential ecological risk, driven by the presence of common compounds as azithromycin in both Tunisian groundwater and surface water systems, underscores the ongoing pressures on the studied basin where agriculture, industry and tourism activities predominate. The findings reinforce the urgent need for increased monitoring frameworks, both regionally and internationally, to better manage and mitigate the impact of CECs on the environment. Additionally, to investigate the fate and transformation pathways of CECs and their TPs in intermittent streams, open-source cheminformatics approaches were applied. A combination lab-scale experiments, data curation and prediction models were used to assess the environmental behaviour of TPs. N-oxide transformation products were found to remain persistent along the stream and were observed to be derived from WWTP point sources rather than in-stream formation. Unfortunately, lab-scale experiments did not successfully predict the high occurrence of N-oxide TPs observed in field studies. Suspect and non-target screening approaches, supported by open-source tools, were performed as complementary and valuable tools, to expand the target analysis and provide a deeper insight of the presence of TPs and other unknowns. These approaches enabled the identification of compounds not initially included in the analytical method, offering a broader understanding of the contaminant profiles in intermittent streams. Overall, the findings presented in this thesis underscore the necessity of interdisciplinary strategies and adaptive water management to protect vulnerable freshwater, both intermittent streams and groundwater resources across the Mediterranean Basin.
Design and regulation of high-performance catalysts in cathodes and separators for alkali metal-sulfur batteries
(Universitat de Barcelona, 2025-10-07) Li, Canhuang; Cabot i Codina, Andreu; Universitat de Barcelona. Facultat de Química
[eng] Alkali metal-sulfur batteries (MSBs) are considered to be the most promising materials to replace lithium-ion batteries (LIBs) in next-generation energy storage systems. Compared to LIBs, lithium sulfur batteries (LSBs) exhibit a six-fold higher theoretical energy density, reaching up to 2500 Wh kg -1, sodium sulfur batteries (SSBs) also demonstrate a theoretical gravimetric energy density of 1274 Wh kg -1, while potassium sulfur batteries (PSBs) achieve a theoretical weight-specific energy density of up to 1023 Wh kg -1. Furthermore, their commercialization costs and environmental impact may be significantly lower. Despite these attractive advantages, the electrical insulating properties of sulfur and Li2S/Na2S/K2S, as well as the shuttle effect of intermediate metal polysulfides (MPS) greatly limit the practical application of AMSBs. In addition, the severe volume change (>80%) and slow redox kinetics during charge and discharge also reduce the cycle life and power density. The rational design and engineering of the catalysts can effectively overcome the above challenges. The state of the art of AMSBs and the targeted requirements from two points of view: physical adsorption and chemical catalysis, are summarized in Chapter 1. Within the results part of this thesis, in Chapter 4, I explore the effects of metal phosphide and heteroatom doping on the separator on the performance of LSBs. In this study, I detail a one- step approach to growing tungsten phosphide (WP) nanoparticles on the surface of nitrogen and phosphorus co-doped carbon nanosheets (WP@NPC). I further demonstrate that this material provides outstanding performance as a multifunctional separator in LSBs, enabling higher sulfur utilization and exceptional rate performance. These excellent properties are associated with the abundance of lithium polysulfide (LiPS) adsorption and catalytic conversion sites and rapid ion transport capabilities. Experimental data and density functional theory (DFT) calculations demonstrate tungsten to have a sulfophilic character while nitrogen and phosphorus provide lithiophilic sites that prevent the loss of LiPSs. Furthermore, WP regulates the LiPS catalytic conversion, accelerating the Li-S redox kinetics. As a result, LSBs containing a polypropylene separator coated with a WP@NPC layer show capacities close to 1500 mAh g-1 at 0.1C and coulombic efficiencies above 99.5 % at 3C. Batteries with high sulfur loading, 4.9 mg cm−2, are further produced to validate their superior cycling stability. Overall, this work demonstrates the use of multifunctional separators as an effective strategy to promote LSB performance. This work was published in Journal of Colloid and Interface Science in 2024. In Chapter 5, I demonstrate the design and production of multifunctional SnSe as a separator for MSBs. More in detail, SnSe nanosheets are introduced as additive into the cathode side of the glass microfiber (GF) separator of the MSB. Taking LSBs as an example, it is demonstrated that the GF-SnSe separator (GF@SnSe) shows strong chemical affinity to LiPSs and superior catalytic activity, inhibiting the transport of LiPSs to the anode and accelerating their conversion. Combining experimental and calculation results, the SnSe additive is shown to decrease the Li2S decomposition energy barrier. Overall, GF@SnSe separators provide significantly improved LSB rate performance and cycling stability with a 0.049% capacity decay per cycle. Besides, the GF@SnSe separator promotes the electrochemical performance of SSBs and PSBs. Overall, this work presents a significant advancement in the development of multifunctional separators in LSBs as well as the emerging Na-S and K-S systems. This work was published in Advanced Energy Materials in 2024. Since two-dimensional (2D) nanocarbon-based materials with controllable pore structures and hydrophilic surfaces have shown great potential in sulfur host materials, in Chapter 6, I present a scalable approach for the preparation of porous ultrathin nitrogen-doped carbon nanosheets decorated with ultrafine FeTe2 nanoparticles (FeTe2/CN), derived from metal–organic frameworks (MOFs) through a mild and modifier-free synthesis strategy. This graphene-like structure serves as a promising cathode material to address complex challenges in LSBs. Experimental results and DFT calculations highlight the distinct advantages of this structure: (1) synergistic adsorption occurs through the lithiophilic sites of CN and the sulfiphilic sites of FeTe2, efficiently capturing LiPS; (2) enhanced conductivity of the CN nanosheets, combined with the robust spin state effect of FeTe2, accelerates electron transfer and reduces energy barriers, thereby improving sulfur redox reaction (SRR) kinetics; (3) the graphene-like CN nanosheets provide numerous active sites and mitigate volume expansion during cycling. Consequently, LSBs based on S@FeTe2/CN cathodes exhibit high initial capacity, exceptional rate performance, and outstanding stability. This work offers a novel strategy for preparing 2D nanocarbon-based materials with highly exposed active sites to enhance SRR efficiency. This work has been published in Energy & Environmental Science in 2025. Building on my previous works, in Chapter 7, I further explore the feasibility of nanomaterials inSSBs. In this study, I demonstrate a heteronuclear diatomic catalyst featuring Fe and Co bimetallic sites embedded in nitrogen-doped hollow carbon nanospheres (Fe–Co/NC) as an effective sulfur host at the cathode of Na–S batteries. Aberration-corrected high-angle annular dark field scanning transmission electron microscopy demonstrates the presence of isolated Fe– Co atomic pairs, while synchrotron radiation X-ray absorption fine structure analysis confirms the (Fe–Co–N6) coordination structure. DFTcalculations show that the introduction of Fe atoms induces electron delocalization in Co(II), shifting the electronic configuration from a low-spin to a higher-spin state. This shift enhances the hybridization of the Co dz2 orbitals with the antibonding π orbitals of sulfur atoms within the sodium sulfide species that accelerates their catalytic conversion. As a result, Fe–Co/NC-based cathodes exhibit excellent cycling stability (378 mAh g–1 after 2000 cycles) and impressive rate performance (341.1 mAh g–1 under 5 A g– 1). This work has been published in the Journal of the American Chemical Society in 2025.
Understanding the sorption of radium and lanthanides in soils and biochars for predictive modelling and remediation purposes
(Universitat de Barcelona, 2025-10-03) Serra Ventura, Joan; Vidal Espinar, Miquel; Rigol Parera, Anna; Universitat de Barcelona. Facultat de Química
[eng] The exponential increase in the demand for certain metals across various technological sectors has intensified mining and industrial activities. A consequence of these processes is the unintentional enrichment of lanthanides (Ln) and naturally occurring radionuclides (NOR), such as radium (Ra), in the resulting waste. The accumulation of these contaminants in aquatic and terrestrial environments, with soils acting as receptors of leachates, raises concerns about ecosystem integrity and human health. Therefore, environmental risk assessment studies are essential to evaluate potential exposure scenarios and risks. A key input parameter in risk assessment models is the solid-liquid distribution coefficient (Kd), which reflects a contaminant’s affinity to bind to soil and provides information on its mobility across environmental compartments. Understanding how Kd values vary with the physicochemical properties of the soil’s solid and liquid phases is fundamental for predicting contaminant behaviour. Both parametric and probabilistic modelling approaches are appropriate for deriving new Kd values. When contaminant concentrations and mobility into the food chain represent an unacceptable risk, remediation actions are recommended. In such cases, the use of sorbent materials, either as soil amendments or water filters, can be an effective strategy for immobilising or removing contaminants. For this reason, there is a growing need to conduct comprehensive studies evaluating the sorption capacity of candidate materials for removing target contaminants. Currently, knowledge regarding the interaction of Ra with soils remains scarce, and no unequivocal conclusions have been established concerning the physicochemical parameters of the soil’s solid and water phases that govern Ra sorption and desorption. The lack of understanding is mainly due to the absence of systematic studies addressing this issue, insufficient physicochemical characterisation of affected compartments, and the lack of a critically reviewed, up-to-date compilation of Kd values enabling consistent statistical analyses. As a result, the development of robust, validated models capable of reliably predicting Kd (Ra) values in soils, as well as the derivation of probabilistic functions describing Kd values distributions grouped according to physicochemical properties, or other relevant criteria, remains a significant challenge. Complementarily, one approach to help address the data gap is identifying chemical analogues from which equivalent interaction data may be derived. Additionally, no systematic studies have yet been performed to evaluate sorbent candidates such as biochars, a carbon-rich material that could offer a sustainable alternative to activated carbon for removing Ln from contaminated waters. In the present thesis, the factors influencing Ra sorption in soils have been identified through the acquisition of new sets of sorption and desorption Kd values across a collection of soils with contrasting properties. Several predictive models have been developed and validated, based on parametric equations that require only a few physicochemical parameters of the solid and liquid phases as input data, such as Kd (Ca + Mg), pH, amorphous Mn content in the soil, or specific surface area. Additionally, an alternative probabilistic approach has been applied, allowing for the estimation of the most probable Kd (Ra) values with minimal characterisation of the environmental matrices involved, requiring only the pH or its soluble Ca and Mg content. To support this approach, both experimentally obtained in the laboratory and critically reviewed literature data, together with available characterisation data, have been compiled to create a Kd (Ra) database with the highest number of entries collected to date. Furthermore, barium has been demonstrated to be a suitable, stable chemical analogue for deriving Ra sorption and desorption Kd data. Through the establishment of correction factors, this approach could help to fill existing data gaps without the need to use Ra radioisotopes, thereby avoiding the generation of radioactive wastes. A systematic study involving various untreated biochars and different experimental sorption approaches has demonstrated the suitability of these materials for remediating sites contaminated with Ln. The maximum sorption capacities and Kd values for Ln have been determined and evaluated under a range of contamination scenarios, from simpler cases, such as those containing only Sm, to more complex ones, involving multiple stressors, such as mixtures of Ln or simulated acid mine drainage containing Ln. The key physicochemical properties of biochar responsible for the effective removal of Ln in complex contamination contexts have been identified. In addition, the main mechanisms involved in the Ln sorption process have been elucidated through the integration of sorption studies with spectroscopic and imaging techniques. Finally, the sorption analogy between different elements of the Ln series has been demonstrated in environmentally relevant matrices, such as carbon-rich sorbent materials, clay minerals, and soils, thus helping to simplify the risk assessment in areas contaminated with Ln.
Phase Separation of the Intrinsically Disordered Activation Domain of the Androgen Receptor and Therapeutic Approaches
(Universitat de Barcelona, 2025-02-11) Bielskutė, Stasė; Salvatella i Giralt, Xavier; Andrògens; Universitat de Barcelona. Facultat de Química
[eng] Transcription factors represent highly attractive therapeutic targets, yet they are among the most challenging due to the intrinsically disordered nature of their activation domains (ADs). In this study, we focus on the intrinsically disordered AD of the androgen receptor (AR), a key therapeutic target in castration-resistant prostate cancer (CRPC), an aggressive form of prostate cancer (PC) with a poor prognosis. EPI-001, a small molecule discovered through phenotypic screening, was the first drug targeting an intrinsically disordered protein (IDP) to enter clinical trials. However, the molecular mechanisms underlying its interaction with the AR AD remain unclear, hindering progress in rational drug design for CRPC. Using various biophysical techniques, we demonstrate that the aromatic nature of the AR AD is critical for both its ability to form biomolecular condensates via liquid- liquid phase separation and its transcriptional activity. This aromatic character also facilitates the translocation of the AR AD to the nucleus and enables its partitioning into transcriptional condensates. Additionally, our study of EPI-001 binding to the AR AD reveals that the aromatic residues and helical propensity of the AR AD are pivotal for its selective interaction with the drug. We found that EPI-001 binding alters the network of contacts within the AR AD, enhancing its oligomerization and increasing the rigidity of the condensates. Also, our findings provide a deeper understanding of the interactions that stabilize AR AD condensates, allowing for the structural optimization of small molecules, leading to greater efficacy compared to EPI-001. Finally, we demonstrate that the AR AD adopts a more ordered secondary structure within the condensates, which might increase the stability of drug-binding sites. Collectively, these insights could not only help to rationalize drug discovery for CRPC but also extend to other diseases where IDPs play a central role.
Mostreig i anàlisi molecular de l’aerosol orgànic a la troposfera baixa: fonts i transformacions
(Universitat de Barcelona, 2025-09-12) Jaén Flo, Clara; Grimalt Obrador, Joan; Van Drooge, Barend L.; Universitat de Barcelona. Facultat de Química
[cat] L’aerosol orgànic (OA) representa una fracció molt variable de les partícules en suspensió (PM), i comprendre les seves propietats químiques, físiques i toxicològiques és essencial per millorar la qualitat de l’aire. En les darreres dècades, s’han identificat diversos compostos orgànics que actuen com a marcadors de fonts d’emissió i processos de transformació atmosfèrics i que poden tenir efectes tòxics. Entre aquests es troben els compostos emesos directament a l’atmosfera, l’aerosol orgànic primari (POA), com els hidrocarburs aromàtics policíclics (PAHs), generats per combustió incompleta de matèria orgànica; els hopans, associats al trànsit rodat; i el levoglucosà, indicador de la crema de biomassa. També s’hi troben compostos formats a l’atmosfera, que constitueixen l’aerosol orgànic secundari (SOA), derivats principalment de l’oxidació de compostos orgànics volàtils com l’isoprè i l’α-pinè. Les condicions meteorològiques influencien la distribució de tots aquests compostos. No obstant això, el coneixement integrat sobre la composició dels aerosols, les condicions atmosfèriques i els seus efectes sobre la salut humana és limitat, especialment en situacions meteorològiques complexes on la dispersió dels contaminants es veu reduïda. Aquesta tesi té com a objectiu identificar fonts d’emissió, processos de transformació i patrons de distribució vertical dels aerosols a la troposfera baixa mitjançant l’anàlisi molecular de compostos orgànics presents a les PM en diversos entorns, alçades i condicions atmosfèriques. Primerament, s’ha desenvolupat una metodologia per analitzar PAHs i compostos polars en mostres de volum baix (<1 m3) mitjançant GC-MS d’alta resolució. Aquesta tècnica de cost baix ha demostrat ser eficient, amb bona repetibilitat i mostra una bona correlació amb l’anàlisi de volums grans, tot reduint el consum de materials i dissolvents. A més, ha obert la porta a un sistema de mostreig amb globus captius a la troposfera baixa consistent en sondejos de tres hores de duració amb l’objectiu d’estudiar la composició orgànica a dues alçades (superfície i ⁓ 400 m). Aquest estudi s’ha dut a terme en entorns industrials, rurals i suburbans i s’ha complementat amb l’anàlisi d’OA a la zona urbana de Barcelona, tot aprofitant la seva orografia. Les concentracions dels compostos orgànics a diferents alçades mostren una acumulació de POA a la superfície, especialment durant les inversions tèrmiques nocturnes. Aquestes observacions suggereixen que les emissions de trànsit i crema de biomassa es concentren a la capa estable nocturna, amb concentracions que poden diferir fins a un ordre de magnitud a les primeres capes de l'atmosfera. Els compostos secundaris, com alguns PAHs oxigenats i el SOA biogènic, presenten una distribució més homogènia a la troposfera baixa, amb concentracions sovint més elevades a la capa residual nocturna. A més, les relacions d’aquests amb els seus precursors suggereixen una oxidació més gran en alçada. En aquesta memòria també s’inclou un estudi conjunt de la composició orgànica de les PM i la toxicitat associada de mostres recollides per autoritats regionals en diverses estacions de monitoratge. Les emissions de vehicles són la font predominant a l’estació urbana de trànsit, mentre que a les zones suburbanes i rurals, la crema de biomassa a l’hivern i el SOA a l’estiu influeixen significativament en la qualitat de l’aire. Les mostres recollides durant l’hivern en zones suburbanes i rurals, riques en aerosols procedents de la crema de biomassa, van provocar la mortalitat més elevada en cèl·lules epitelials pulmonars exposades. Aquests resultats destaquen la necessitat d’estratègies específiques adaptades a cada entorn per millorar la qualitat de l’aire arreu del territori. Finalment, el treball amplia la perspectiva a un punt elevat a Sierra Nevada (2500 msnm), on s’han identificat diverses fonts i processos a partir de la composició orgànica i inorgànica de les PM. Aquests estan clarament associats a circulacions típiques de zones muntanyoses i de gran escala, com ara el transport de brises de muntanya i les intrusions de pols sahariana. En general, els resultats mostren la forta influència de l’oxidació i del transport d’aerosols de mig i llarg abast sobre la composició química de l’aerosol en aquest lloc elevat.
Microbial Biochemistry of Emerging Contaminants and Anthropogenic Organic Matter in the Atlantic and Southern Oceans
(Universitat de Barcelona, 2025-05-21) Iriarte Martinez, Jon; Dachs, Jordi; Vila-Costa, Maria; Universitat de Barcelona. Facultat de Química
[eng] The introduction of anthropogenic organic chemicals into the environment, particularly those exhibiting persistence, bioaccumulation, potential for long-range transport, and toxicity, poses a threat to the well-being of the Earth system. The global ocean, a vital component that sustains life, is especially vulnerable as it often serves as the main sink for these contaminants. In the marine environment, classic pollutants such as the polycyclic aromatic hydrocarbons (PAHs) and emerging contaminants like the organophosphate esters (OPEs) and the per- and polyfluoroalkyl substances (PFAS) compose the anthropogenic dissolved organic carbon (ADOC) pool. The fate of these compounds is governed by complex interactions between physicochemical and biological processes, with the marine microbial communities potentially playing a relevant role, as they do in the marine biogeochemical cycles. However, their role in processing background contaminant concentrations in the open ocean, as well as the effects of these compounds on marine microbes, remains poorly studied. This thesis explores the impact of background concentrations of organic contaminants—including PAHs, OPEs, and PFAS—on marine microbial communities and their role in the biodegradation of these pollutants in the global ocean. Focusing on remote regions like coastal Antarctica and the open ocean, the works presented in this thesis integrate chemical data on contaminant concentrations with compositional and functional data on marine microbial communities, as well as other physicochemical parameters, obtained from field measurements and experiments, to investigate the interactions between contaminants and microbial communities under real oceanic conditions. In coastal Antarctica, significant correlations were found between contaminant concentrations and microbial composition, highlighting complex biogeochemical controls at low contaminant levels. The results of this thesis provide the largest dataset on PAH and PFAS concentrations in coastal Antarctica, revealing substantial temporal and spatial variability linked to snowmelt and geographical features. They also show that PAH biodegradation is enhanced by snowmelt-induced bacterial activity, while microbial-mediated desulfurization may serve as a PFAS sink. In addition, aromatic hydrocarbon-degrading genes were identified across diverse marine microorganisms using a curated bioinformatic approach with metagenomic datasets, indicating a widespread potential for PAH biodegradation in temperate and tropical oceans. Assessment of the gene abundance and PAH concentrations showed a negative correlation with the low molecular weight fraction of the PAHs. Furthermore, background concentrations of PAHs were found to be a significant factor explaining variation in the bacterial community composition, together with other previously described environmental drivers of microbial communities such as temperature and nutrient concentrations. Field experiments revealed significant biodegradation of highly hydrophobic OPEs in the Atlantic Ocean, linked to increased bacterial protein production, marking the first open-ocean evidence of OPE biodegradation under natural conditions. This thesis demonstrates that concurrent characterization of organic contaminants and microbial communities through field-based measurements provides accurate insights into the complexity of real environmental conditions. It reveals that background levels of organic contaminants, while not the main drivers, have the potential to influence marine microbial communities significantly. Additionally, microbial degradation was observed to be a potential oceanic sink for emerging contaminants in the surface ocean. These findings highlight the need for further research on biodegradation rates and the impact of contaminants on marine biogeochemical cycles. Understanding these processes is essential for accurate risk assessments, especially given the rising release of anthropogenic compounds and the intensification of climate change-related stressors.
A Multiscale Approach to Unravelling the Structure and Infrared Spectra of Astronomically Relevant Nanosilicates
(Universitat de Barcelona, 2025-07-15) Mariñoso Guiu, Joan; Bromley, Stefan Thomas; Universitat de Barcelona. Facultat de Química
[eng] Silicates are ubiquitously found both terrestrially and throughout the universe where they are often found as small particles. In the interstellar medium (ISM), these particles undergo high-energy processes that cause them to shatter into ultrasmall grains, resulting in a vast population of nanosilicates. These nanosized grains are likely to play a crucial role in various chemical processes in space, such as catalysing the formation of molecules. Infrared (IR) spectroscopy is the primary tool for identifying silicate grains and analysing their properties and chemical composition. Such analyses are typically performed by empirical comparisons of astronomical observations with spectra of laboratory-made samples. However, this approach only provides indirect information about atomistically detailed properties and typically employs bulk silicate samples. Consequently, most knowledge about nanosilicates relies on top- down extrapolations from bulk properties. As such, much of our current understanding of nanosilicate grains is likely to be unreliable due to the known strong size dependence of structure and properties of materials at the nanoscale. Thanks to the advances in technology and theoretical methods, computational modelling has revolutionized our ability to interpret experimental results and astronomical observations. In particular, such modelling can probe materials at conditions that are challenging to replicate in the laboratory. (e.g. at very small sizes and under extreme environments). In the case of nanosilicates, computational modelling offers a powerful alternative approach to improve our understanding of their properties and to potentially help confirm their presence and abundance in the universe together with astronomical observations and laboratory experiments. This thesis expands upon previous theoretical models to study nanosilicates aiming to provide a more comprehensive study of their properties. Here, the main particular focus is on improving our knowledge and understanding of these nanosystems through their IR spectra. The thesis is structured as follows: first, a general overview of silicates, their astronomical significance, and the important role of nanosilicate grains is presented, along with a review of the current state-of-the-art computational modelling approaches. Next the theoretical foundations of all the methodologies used to build our models are described in depth, as well as the different software used. Afterwards, the different research publications derived from this work are discussed providing, for each one, an introduction to the theme and motivation of the publication and a brief discussion of the results and the conclusions that can be extracted from them. First, we explore various methodologies for accurately computing vibrational spectra, emphasizing their ability to incorporate thermal effects. We then compute the heat capacities of small nanograins comparing them with previous estimates and analysing the implications for their IR emission. Next, we investigate the properties of slightly hydroxylated nanosilicates, particularly their ability to emit microwave radiation. This is followed by a collaborative study combining computational and observational modelling to assess the potential detectability of small nanosilicate grains using. We further discuss two additional collaborative works to study cationic and anionic nanosilicates synthetized in the lab, examining their relevance to both astronomy and atmospheric chemistry. Finally, we study the size dependency of different nanosilicate properties, including IR spectra through modelling nucleated nanosilicate growth. The thesis concludes with a summary of the main conclusions derived from these works.
Electronic Structure Engineering for Enhanced Additive Performance in Robust Sulfur Cathodes
(Universitat de Barcelona, 2025-07-17) Huang, Chen; Cabot i Codina, Andreu; Zhang, Chaoqi; Universitat de Barcelona. Facultat de Química
[eng] The doctoral thesis was authored by PhD candidate Chen Huang at the Catalonia Institute for Energy research (IREC) between 2022 and 2025, with funding provided by the China Scholarship Council. The thesis primarily focuses on electron modulation engineering for optimizing active cathode host materials in high-performance metal-sulfur batteries (MSBs). Comprising eight main chapters, the paper begins with an overarching introduction to MSBs, highlighting the current challenges and the research efforts aimed at overcoming them. Chapter 2 outlines the objectives of the paper, while Chapter 3 details the experimental methods employed. Chapters 4 through 7 delve into the complexities of MSB, discussing in depth the various strategies devised to address common challenges. These strategies include: (i) Designing heterostructures and vacancies engineering (ii) Creating homologous heterogeneous structures (iii) Developing P-N heterogeneous engineering (iv) Preparing hollow structure (v) Introducing anion doping strategies. In Chapter 4, the thesis focuses on the synthesis of a ZnTe/CoTe2 composite material with vacancies and heterostructures. The incorporation of vacancies enhances the conductivity of the electrode material, while the designed heterostructure facilitates Li+ diffusion. In Chapter 5, the hollow homogeneous heterostructure NiS2/NiSe2@NC host material is employed in LSBs, promoting changes in the Ni3+ spin state. Chapter 6 focuses on the generation of Se vacancies and lattice distortion in Bi2Se3@C via introduction doping strategies. Finally, Chapter 7 explores a P-N heterojunction strategy through the synthesis of Co3O4-NC@C3N4 electrode materials, elucidating the electron transfer mechanism and the spin effect on Co3+.
Understanding the role of incidental nanoparticle properties as determinants of industrial workplace exposures
(Universitat de Barcelona, 2025-07-17) Moreno Martín, Verónica; Viana Rodríguez, María del Mar; Macarulla Martí, Marcel; Universitat de Barcelona. Facultat de Química
[eng] The dynamic nature of nanoparticles (NPs), marked by continuous transformations in their physical and chemical properties, makes NPs distinct from other pollutants. Although these particles do not contribute significantly to overall airborne particle mass concentrations, they are dominant in terms of particle number concentrations (N) in urban air in most regions of the world. NPs have been associated with adverse effects on human health, they are capable of penetrating deep into the respiratory tract causing pulmonary inflammation and can translocate to the bloodstream and cross body membrane barriers. From the point of view of their emission sources, NPs may be natural or anthropogenic, the latter originating from human activity. Anthropogenic NPs may be engineered or incidentally generated (INPs) as a result of anthropogenic activities from machinery, vehicles and combustion sources. In general, engineered nanomaterials are manufactured with specific properties in terms of size, morphology, and chemical composition while INPs are characterised by undetermined attributes which can only be determined experimentally and onsite. Moreover, there is a significant difference in human awareness: workers are generally aware of the engineered nanomaterials they handle but are often unaware of the exposure to INPs generated during industrial processes. In this framework, exposure to NPs can be assessed using field monitoring campaigns, prediction models, and/or laboratory experiments. At present, no legally-binding occupational exposure limits (OELs) are available for NPs in EU or international regulatory frameworks, thus limiting the assessment and control of risks in workplace environments. Due to the diversity of industrial processes which generate NPs, a comprehensive assessment of NP emissions and properties in real-world scenarios remains necessary. This Thesis aims to contribute to the understanding of the role of incidental nanoparticles (INPs) as determinants of workplace exposure. In this framework, an integrated assessment of exposure in selected industrial scenarios is proposed, covering the characterisation of NP emission sources, an exhaustive analysis of NP properties in the workplace, and the application of modelling tools to assist facilities in exposure management and minimisation. To achieve this, three main objectives were set: I) To investigate the emission mechanisms of INPs during industrial activities in the ceramic sector; II) to evaluate worker exposure to incidental NPs during specific industrial activities linked to the ceramic industry, with a special focus on physico-chemical and toxicological characterisation; and III) to assess the potential of reduced order models (ROMs) to estimate INPs emissions and optimise industrial processes to enhance worker safety. In this framework, airborne INPs were assessed across three industrial scenarios — tile cutting, tile firing, and thermal spraying — representing distinct NP generation processes of mechanical and thermal nature. The results of this Thesis are presented in the form of three publications (two published and one under review). The first publication focuses on understanding the particle formation, release mechanisms, and properties of INPs generated during rotary-dry cutting of ceramic tiles. The second study investigates particle number concentrations, chemical composition, morphology, and in vitro cytotoxicity of INPs released during ceramic tile firing. Finally, in the third study a ROM was applied to investigate the model’s potential to optimise the ventilation system, enhance energy savings and reduce the carbon footprint while maximising worker respiratory safety by minimising INP exposures. The results from this Thesis highlight that current occupational exposure regulations predominantly focus on coarser particle sizes do not adequately address the health risks associated with NPs, emphasising the need for internationally agreed NP occupational limit values, supported by harmonised methodologies for exposure characterisation. Accordingly, the findings presented in this Thesis aim to support the development of such a regulatory framework by providing insights into INP exposure and its potential implications for workers’ health. The assessment of cell viability after exposure to PM2 aerosols collected in two of the case studies highlights the potential health risks associated with INP exposure, particularly in tile cutting and tile firing. The findings emphasise the importance of characterising the toxicological properties of aerosols collected in situ, rather than relying on pristine NPs. This underscores the need for improved sampling methods that minimise artefacts while preserving aerosol physical and chemical properties. In addition, the variability in aerosol size distribution and elemental composition are identified as crucial factors influencing the cytotoxicity of airborne aerosols. These results highlight the importance of adapting methods for NP sampling in real-world settings. It is concluded that the determination of IC50 and IC10 values provide valuable tools for integrating these results into risk assessment frameworks, helping to develop targeted safety measures to protect workers from NP exposure. Furthermore, the application of the ROM to a thermal spraying facility highlights its potential for optimising ventilation systems, thereby supporting both worker safety and operational efficiency, and offering a pathway for companies to align with potential future regulations.
Selective scintillation resins for radioactivity analysis: From extractant development to method application
(Universitat de Barcelona, 2025-06-27) Giménez Guerra, Isaac; Tarancon Sanz, Alex; Bagán Navarro, Héctor; Universitat de Barcelona. Facultat de Química
[eng] The present PhD thesis focuses on developing innovative strategies for the fast, accurate, reliable, and environmentally friendly determination of radionuclides. This has included developing new scintillating materials and analytical methodologies that address the limitations of current conventional methods. For this purpose, two different selective scintillating materials were developed. The first one was a PSresin intended for the determination of the gross alpha parameter (α‐ PSresin), and included the synthesis and optimization of the used extractant, its immobilization, and the scaling‐up for commercial purposes. The second material was a scintillating ion imprinted polymer for 55Fe, being the first selective and scintillating imprinted material for radioanalytical purposes. Additionally, the potential of computational tools for the design of new extractants was evaluated, demonstrating their effectiveness in reducing development costs and time. From the analytical point of view, specific working methodologies have been developed providing satisfactory results and becoming a green and fast alternative for radionuclide determination compared to conventional methods. In particular, a new analytical method has been developed for the gross alpha parameter using the α‐PSresin developed in this PhD thesis. Furthermore, novel analytical methods were established for the determination of plutonium isotopes and radiostrontium using the existing AL‐ PSresin and CE‐PSresin, respectively. In addition, sequential methodologies allowing the tandem determination of these radionuclides were also successfully developed using both PSresins in combination. The application of the developed methodologies for radionuclide analysis in this study have demonstrated to reduce the analysis time, cost and use of toxic reagents compared to the conventional methods, all while keeping equal or lower limits of detections. These methods represent an accurate and reliable alternative for environmental monitoring and decommissioning purposes, with the added benefit of being environmentally conscious.

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