Molecular dynamics (MD) simulations based on the multistate empirical valence bond model have been performed to study the proton transfer (PT) process in aqueous solution. This study focuses on the details of the hydrogen bond (HB) dynamics in the solvation shells of an excess proton accompanied by PT events. The HB dynamics analyses show that the three water molecules in the first solvation shell of hydronium (HO) tend to break their accepted HB to maintain a distorted Eigen (HO) configuration. The results from MD simulations show that the cleavage and formation of accepted HBs on the water ligands in the first solvation shell of the proton acceptor water molecule and donor water molecule are crucial to drive the PT. Moreover, the water-donated and -accepted HBs around the HO solvation shells are inequivalent, induced by the excess proton. Coupled with the PT, the donated HBs are enhanced on the proton acceptor side, while, in contrast, the accepted HBs are weakened on the same side.
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Acc Chem Res
January 2025
Department of Chemistry , University of California, Berkeley, California 94720, United States.
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View Article and Find Full Text PDFJ Phys Chem A
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Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.
Theoretical simulations of electron detachment processes are vital for understanding chemical redox reactions, semiconductor and electrochemical properties, and high-energy radiation damage. However, accurate calculations of ionized electronic states are very challenging due to their open-shell nature, importance of electron correlation effects, and strong interactions with chemical environment. In this work, we present an efficient approach based on algebraic diagrammatic construction theory with polarizable embedding that allows to accurately simulate ionized electronic states in condensed-phase or biochemical environments (PE-IP-ADC).
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Ufa Institute of Chemistry, Ufa Federal Research Centre of the Russian Academy of Sciences, Laboratory of Physicochemical Methods of Analysis, 69 Prospekt Oktyabrya, Ufa 450054, Russian Federation.
The first-stage acid-base equilibrium of 5,5,6-trihydroxy-6-methyldihydropyrimidine-2,4(1,3)-dione was studied for the first time in aqueous solutions. Its constant (pK = 9.23 ± 0.
View Article and Find Full Text PDFAcc Chem Res
January 2025
Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.
ConspectusWater-in-salt electrolytes (WiSEs) are promising electrolytes for next-generation lithium-ion batteries (LIBs), offering critical advantages like nonflammability and improved safety. These electrolytes have extremely high salt concentrations and exhibit unique solvation structures and transport mechanisms dominated by the formation of ion networks and aggregates. These ion networks are central to the performance of WiSEs, govern the transport properties and stability of the electrolyte, deviating from conventional dilute aqueous or organic electrolytes.
View Article and Find Full Text PDFNucleic Acids Res
December 2024
Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France.
The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites as observed in a recent cryo-EM 1.
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