Protonation pattern strongly affects the properties of molecular systems. To determine protonation equilibria, proton solvation free energy, which is a central quantity in solution chemistry, needs to be known. In this study, proton affinities (PAs), electrostatic energies of solvation, and pKA values were computed in protic and aprotic solvents. The proton solvation energy in acetonitrile (MeCN), methanol (MeOH), water, and dimethyl sulfoxide (DMSO) was determined from computed and measured pKA values for a specially selected set of organic compounds. pKA values were computed with high accuracy using a combination of quantum chemical and electrostatic approaches. Quantum chemical density functional theory computations were performed evaluating PA in the gas-phase. The electrostatic contributions of solvation were computed solving the Poisson equation. The computations yield proton solvation free energies with high accuracy, which are in MeCN, MeOH, water, and DMSO -255.1, -265.9, -266.3, and -266.4 kcal/mol, respectively, where the value for water is close to the consensus value of -265.9 kcal/mol. The pKA values of MeCN, MeOH, and DMSO in water correlates well with the corresponding proton solvation energies in these liquids, indicating that the solvated proton was attached to a single solvent molecule.
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Bioinform Adv
December 2024
Structural and Computational Biology Group, Nutritional and Industrial Biochemistry Research Unit, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria.
Motivation: Investigating novel drug-target interactions is crucial for expanding the chemical space of emerging therapeutic targets in human diseases. Herein, we explored the interactions of dipeptidyl peptidase-4 and protein tyrosine phosphatase 1B with selected terpenoids from African antidiabetic plants.
Results: Using molecular docking, molecular dynamics simulations, molecular mechanics with generalized Born and surface area solvation-free energy, and density functional theory analyses, the study revealed dipeptidyl peptidase-4 as a promising target.
J Chem Inf Model
January 2025
Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada.
The near neutral p of histidine is commonly exploited to engineer pH-sensitive biomolecules. For example, histidine mutations introduced in the complementarity-determining region (CDR) of therapeutic antibodies can enhance selectivity for antigens in the acidic microenvironment of solid tumors or increase dissociation rates in the acidic early endosomes of cells. While solvent-exposed histidines typically have a p near 6.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China.
The fundamental hydrolysis behavior of tetravalent actinide cations (An) with a high charge is crucial for understanding their solution chemistry, particularly in nuclear fuel reprocessing and environmental behavior. Using Th as a reference of the An series, this work employed both the periodic model and the cluster model to calculate the first hydrolysis reaction constant (p) of the Th aqua ion and conducted a detailed evaluation of these approaches. In the periodic model, molecular dynamics (AIMD) simulations of Th in the explicit solvation environment are conducted, using metadynamics and constrained molecular dynamics to calculate p values.
View Article and Find Full Text PDFAnal Chem
January 2025
School of Petrochemical Engineering, Liaoning Petrochemical University, Fushun 113001, China.
Chiral discrimination is an indispensable tool that has pivotal importance in the assignment of absolute configuration and determination of enantiomeric excess in chiral compounds. A series of enantiomerically pure -1,2-diaminocyclohexane (-DACH)-derived benzamides were first synthesized by simple chemical steps, and 14 variated derivatives have been assessed as NMR chiral solvating agents (CSAs) for discrimination of the signals of mandelic acid (MA) in H NMR analysis. The highly efficient chiral recognition of CSA on different substrates, including MAs, carboxylic acids, amino acid derivatives, and phosphoric acids (32 examples), was expanded via H, F, and P NMR spectroscopy.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
January 2025
Institute of Energy Material Science, University of Shanghai for Science and Technology, Shanghai, 200093, China.
Rechargeable zinc batteries (RZBs) are hindered by two primary challenges: instability of Zn anode and deterioration of the cathode structure in traditional aqueous electrolytes, largely attributable to the decomposition of active HO. Here, we design and synthesize a non-flammable water-in-dimethyl sulfoxide electrolyte to address these issues. X-ray absorption spectroscopy, in situ techniques and computational simulations demonstrate that the activity of HO in this electrolyte is extremely compressed, which not only suppresses the side reactions and increases the reversibility of Zn anode, but also diminishes the cathode dissolution and proton intercalation.
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