The Helmholtz free energy, energy, and entropy of mixing of ,-dimethylformamide (DMF) and water are calculated in the entire composition range by means of Monte Carlo computer simulations and thermodynamic integration using all possible combinations of five DMF and three widely used water models. Our results reveal that the mixing of DMF and water is highly non-ideal. Thus, in their dilute solutions, both molecules induce structural ordering of the major component, as evidenced by the concomitant decrease in the entropy. Among the 15 model combinations considered, only 4 reproduce the well-known full miscibility of DMF and water, 3 of which strongly exaggerate the thermodynamic driving force of the miscibility. Thus, the combination of the CS2 model of DMF and the TIP4P/2005 water model reproduces the properties of the DMF-water mixtures far better than the other combinations tested. Our results also reveal that moving a fractional negative charge from the N atom to the O atom of the DMF molecule, leading to the increase in its dipole moment, improves the miscibility of the model with water. Starting from the CS2 model and optimizing the charge to be moved, we propose a new model of DMF that reproduces very accurately both the Helmholtz free energy of mixing of aqueous DMF solutions in the entire composition range (when used in combination with the TIP4P/2005 water model) and also the internal energy of neat DMF.
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http://dx.doi.org/10.1021/acs.jpcb.1c01749 | DOI Listing |
J Biochem Mol Toxicol
January 2025
Department of Medical Biochemistry, Faculty of Medicine, Kahramanmaraş Sütçü İmam University, Kahramanmaraş, Turkey.
Neurodegenerative diseases are significant health concerns that have a profound impact on the quality and duration of life for millions of individuals. These diseases are characterized by pathological changes in various brain regions, specific genetic mutations associated with the disease, deposits of abnormal proteins, and the degeneration of neurological cells. As neurodegenerative disorders vary in their epidemiological characteristics and vulnerability of neurons, treatment of these diseases is usually aimed at slowing disease progression.
View Article and Find Full Text PDFCommun Biol
January 2025
Faculty of Science, Ibaraki University, Mito, Japan.
Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and photosynthetic strategies employed by phototrophic extreme halophiles that enable them to thrive in hypersaline environments. Here we present the cryo-EM structures of (1) a unique native Hlr.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Physics and Competence Centre for Catalysis, Chalmers University of Technology, SE-412 96, Göteborg, Sweden.
The performance of Cu-exchanged chabazite (Cu-CHA) for the ammonia-assisted selective catalytic reduction of NO (NH-SCR) depends critically on the presence of paired complexes. Here, a machine-learning force field augmented with long-range Coulomb interactions is developed to investigate the effect of Al-distribution and Cu-loading on the mobility and pairing of complexes. Performing unbiased and constrained molecular dynamics simulations, we obtain unique information inaccessible to first-principle calculations and experiments.
View Article and Find Full Text PDFEur J Pharmacol
January 2025
Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan; Department of Pharmacy, Korea University, Sejong 20019, South Korea. Electronic address:
The study investigated the anxiolytic, antidepressant, sedative/hypnotic and in silico molecular docking properties of the synthetic ephedrine-based derivative of thiourea, 3-benzothioyl-1-(3-hydroxy-3-phenyl-3-propyl)-1-methylthiourea. Safety profile of the compound at various doses was determined in an acute toxicity test. Results showed significant anti-anxiety effects of the compound in all mice studies.
View Article and Find Full Text PDFJ Proteomics
January 2025
Departamento de Bioquímica e Biologia Molecular, Programa de Pós-Graduação em Bioquímica, Universidade Federal do Ceará, Fortaleza, Brazil. Electronic address:
We analyze the proteome changes during the development of the carnauba palm (Copernicia prunifera) seedlings under skotomorphogenic conditions, by separating the embryo into its two components: haustorium (HA) and cotyledonary petiole (CP) and established the descriptive and quantitative proteomes of these tissues across four developmental stages. 5205 proteins were identified in HA and 6028 in CP. These proteomes are rich in proteins known to maintain the skotomorphogenic state, and in a complete set of proteins involved in cellular respiration and biosynthesis of secondary metabolites.
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