Employing a sequential quantum mechanical/molecular mechanical approach for polar protic solvents, we study the absorption spectrum of eumelanin building blocks including monomers, dimers, and tetramers in pure water and methanol and three water-methanol binary mixtures having water molar fractions (Xw = 0.25, 0.50, and 0.75). The binary mixture of solvents is a common situation in experiments, but theoretical studies are limited to the use of continuum models. Here, we use explicit solvent molecules, and specific solute-solvent interaction is analyzed and seen to play an important role. Effects of the electronic polarization of solute by the environment were included using a reliable iterative scheme. The results illustrate that the monomers, dimers, and tetramers are preferably solvated by methanol, but the composition of the mixture in the vicinity of the solute molecules is different from the bulk composition with a preferential microsolvation (hydrogen bonds) in water for most species considered. It is observed that the short-range electrostatic polarization effects of the hydrogen bonds lead to a slight blue shift of the excitation energies when the concentration of water in the mixture is enhanced. For the same species, there is an enhancement of the higher-energy absorption intensity caused by long-range electrostatic interactions with the environment and that the behavior of the experimental spectrum, which is characterized by a nearly monotonic decay from the ultraviolet to the infrared, is qualitatively reproduced by the superposition of the absorption spectra of monomers, dimers, and tetramers in the liquid phase.
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http://dx.doi.org/10.1063/5.0065723 | DOI Listing |
Phys Chem Chem Phys
January 2025
Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
A theory of singlet fission in carotenoid dimers is presented which aims to explain the mechanism behind the creation of two uncorrelated triplets. Following the excitation of a carotenoid chain "bright" B+u state, there is ultrafast internal conversion to the intrachain "dark" 1B-u triplet-pair state. This strongly exchange-coupled state evolves into a pair of triplets on separate chains and spin-decoheres to form a pair of single, unentangled triplets, corresponding to complete singlet fission.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, A-6020 Innsbruck, Austria.
Peptide bond formation from the pure protonated glycine dimer, H(Gly), and from the mixed protonated glycine-diglycine dimer, HGly(Gly), was recently found experimentally to occur in gas-phase experiments in the absence of any catalyst and especially under anhydrous conditions [, 2023, , 775]. In this contribution we further examine the conditions of such unimolecular reactions by means of density-functional theory calculations at the DFT/M06 2X/6-311G++(2df,p) level, focusing in particular on the role played by the protonation site. Two pathways, stepwise and concerted, are identified for the pure protonated dimer, and six pathways are examined for the mixed dimer.
View Article and Find Full Text PDFJ Biol Chem
January 2025
Dept of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India. Electronic address:
Noncoding small RNAs are essential for modulating bacterial gene expression, especially under carbon and nutrient-limited conditions. In this study, by employing both in silico and molecular hybridization tools, we identified a carbon source responsive small RNA in A. baumannii DS002.
View Article and Find Full Text PDFMolecules
December 2024
Department of Chemical Science and Technologies, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 00133 Rome, Italy.
Using the framework of an investigation of the stimuli-responsive behavior of peptide assembly on a solid surface, this study on the behavior of a chemisorbed peptide on a gold surface was performed. The studied peptide is a dimeric form of the antimicrobial peptide Trichogin GAIV, which was also modified by substituting the glycine with lysine residues, while the N-terminus octanoyl group was replaced by a lipoic one that was able to bind to the gold surface. In this way, a chemically linked peptide assembly that is pH-responsive was obtained because of the protonation/deprotonation of the sidechains of the Lys residues.
View Article and Find Full Text PDFJ Mol Biol
January 2025
Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address:
BMP-9 and BMP-10 are TGF-β family signaling ligands naturally secreted into blood. They act on endothelial cells and are required for proper development and maintenance of the vasculature. In hereditary hemorrhagic telangiectasia, regulation is disrupted due to mutations in the BMP-9/10 pathway, namely in the type I receptor ALK1 or the co-receptor endoglin.
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