Dipòsit Digital de la Universitat de Barcelona
El Dipòsit Digital de la Universitat de Barcelona és el repositori institucional que conté en format digital els materials derivats de l'activitat docent, investigadora i institucional de la comunitat universitària.
Enviaments recents
ArticleConformational sampling of seven-membered rings using extended puckering collective variables in metadynamics(American Institute of Physics (AIP), 2025-09-24) Sagiroglugil, Mert; Nin Hill, Alba; Rovira i Virgili, CarmeSeven-membered rings, though scarce in biosynthetic pathways, are increasingly recognized as conformationally rich scaffolds for engineered enzymes and drug leads. Accurately capturing their flexibility requires the use of enhanced-sampling methods. Here we present a set of collective variables (CVs) for metadynamics simulations that extend the Cremer–Pople puckering coordinates to seven-membered rings, and we validate them on cycloheptane and other molecules of increasing complexity (buxenine-G, two azepane derivatives, and ε-caprolactone). The new CVs can be used directly in PLUMED—a popular open-source library for enhanced-sampling and free-energy methods—so they can be used directly in metadynamics workflows. They allow the investigation of conformational transitions, the identification of metastable states, and the mapping of free-energy landscapes of any seven-membered-ring molecule. This provides a quantitative framework for probing the conformational behavior of flexible seven-membered scaffolds and will aid in the rational design of conformationally locked substrates for enzyme engineering and related applications.- ArticleSpin coherence and electron spin distribution of a Silver(II) S = ½ molecular system(American Chemical Society, 2025-06-11) Serra, Judit; Salvadori, Enrico; Liao, Yu-Kai; Gallen Ortiz, Albert; Escuer Fité, Albert; Chiesa, Mario; Mayans Ayats, JúliaThe spin–lattice relaxation time, spin coherence, and spin distribution have been studied through ac susceptometry, pulse EPR, and ultralow-frequency Raman spectroscopy on a silver(II)-derived molecular system with spin 1/2. The combination of magnetometry and spectroscopy techniques demonstrates the occurrence of slow spin magnetic relaxation induced by a spin–phonon interaction. The magnetic behavior and the spin coherence of this AgII-derived system open the door to a new cation into the scarce family of S = 1/2 slow magnetic relaxing systems for further applications in quantum technologies.
- ArticleMultiscale and Multimodal Image Fusion. Coping with Differences in Scanned Area and Spatial Resolution for Raman/Fluorescence Images of Labeled Cells(American Chemical Society, 2025-05-26) Sicre Conesa, Albert; Marsal, Maria; Gómez Sánchez, Adrián; Loza Álvarez, Pablo; Juan Capdevila, Anna deMultiscale and multimodal image fusion is a challenge derived from the diversity of chemical and spatial information provided by the current hyperspectral image platforms. Efficient image fusion approaches are essential to exploit the complementary chemical information across different zoom scales. Most current image fusion algorithms tend to work by equalizing the spatial characteristics of the platforms to be combined, i.e., downsampling pixel size and cropping noncommon scanned sample areas if required. In this work, a new image unmixing algorithm based on a flexible mathematical framework is proposed to enable working with all available image information while preserving the original spatial properties of every imaging measurement. The algorithm is tested on a challenging image fusion scenario of fluorescence and Raman images collected on labeled HeLa cells. The system is relevant from an analytical point of view, since smart fluorescence labeling allows profiting from the excellent morphological information without causing interferences in the rich chemical information furnished by Raman. From a data handling perspective, it offers a challenging multiscale problem, where the fast fluorescence imaging acquisition allows recording full cell images, and the slower Raman image acquisition is focused on scanning only relevant small regions of the cells analyzed. By applying the image fusion algorithm proposed, an improved morphological and chemical characterization of cell constituents in the full cell area is obtained despite the different spatial scales used in the original imaging measurements.
- ArticleAqueous Solid-Phase Peptide Synthesis (ASPPS) using Standard Fmoc/tBu-Protected Amino Acids(American Chemical Society, 2025-11-17) Phungula, Amanda; Kumar, Ashish; Kaushal, Mani; Tucker, Charles; Chen, Lin; Torre, Beatriz G. de la; Albericio Palomera, FernandoIn the context of growing environmental concerns and regulatory pressures, the peptide synthesis community is increasingly turning its attention to green chemistry. Traditional solid-phase peptide synthesis (SPPS), although widely used in research and industry, heavily relies on hazardous solvents, particularly N,N-dimethylformamide (DMF), which poses sustainability and safety issues. Despite various efforts to replace DMF with greener solvents or solvent mixtures, limitations remain, especially for synthesizing medium to large peptides. Aqueous solid-phase peptide synthesis (ASPPS) has emerged as a promising alternative, yet progress has been hampered by the poor solubility of standard Fmoc-amino acids and the instability of newly designed water-compatible protecting groups. Recent developments, such as more soluble protected amino acids and Fmoc-amino acid nanoparticles, have shown potential to overcome these obstacles in ASPPS but have the disadvantage of requiring distinct protected amino acids and/or nonstandard manipulations. Here we present a novel ASPPS protocol that closely mirrors conventional SPPS strategies while being performed entirely in aqueous media. This method utilizes standard Fmoc-protected amino acids and hydrophilic resins. Our findings offer a potential scalable, environmentally friendly approach to peptide synthesis that addresses key limitations of current green methodologies, opening new avenues for sustainable pharmaceutical manufacturing.
- Articleπ-π Stacking Determines the Selectivity of Unnatural DNA Base Pairs Even without Polymerase(American Chemical Society, 2026-01-01) Noori, Zahra; Bermejo, Andreu; Bofill i Villà, Josep M.; Poater i Teixidor, JordiExpanding the genetic alphabet requires a mechanistic understanding of how synthetic bases are faithfully replicated alongside natural DNA. We present a quantum chemical study reproducing the experimentally observed single-nucleotide incorporation selectivity of Hirao’s unnatural base pairs (UBPs) by the 3′–5′ exonuclease-deficient Klenow fragment of Escherichia coli DNA polymerase I. Our analysis focuses on the highly selective DsPx pair, benchmarking its behavior against canonical Watson–Crick pairs and other UBPs. Strikingly, the observed selectivity emerges without explicitly modeling the polymerase, relying solely on computed stacking energies within the DNA helix. Molecular orbital and energy-decomposition analyses show that both electrostatic and dispersion interactions strengthen DsPx’s affinity more, capturing experimental fidelity trends and explaining its superior performance relative to related systems. We further evaluate other selective UBPs, including QPa, DsPa, and DsPn. Together, these results provide a quantitative framework for UBP incorporation selectivity and highlight the crucial role of noncovalent interactions in stabilizing synthetic bases within DNA. By bridging computation and experiment, this work advances design principles for synthetic genetic systems and contributes to unraveling the molecular origins of DNA replication fidelity.