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Halogenated nucleotides have been reported as emerging disinfection byproducts in drinking water and the identification of halogenated nucleotides is a challenging but worthwhile endeavor due to their high risk, diverse chemical structures and scarcity of chemical standards. To improve the recognition efficiency of halogenated nucleotides in complex environmental matrices with multiple halogen ions, a fragmentation pattern-based nontargeted screening strategy was developed, which combines halogen isotope features and characteristic product ions to identify halogenated nucleotides within extensive datasets from high-resolution mass spectrometry. The data were preliminary screened based on the halogen isotope features of chemicals with varying halogen atom counts, followed by further identification using shared fragments with m/z values of 78.96, 96.97 and 211.00 Da. We tentatively identified 72 halogenated nucleotides, including 9 brominated, iodinated and mixed halogen-substituted nucleotides that were annotated and reported for the first time. The effectiveness of the nontargeted identification strategy was demonstrated through manual verification of parent and product ions. Additionally, by comparing the Gibbs free energies of reactions (ΔG) of forming chlorinated, brominated and iodinated nucleotides, chlorinated nucleotides were revealed to exhibit the greatest formation potential, followed by brominated and iodinated nucleotides. 8-Chloroadenosine 5'-monophosphate was selected for the cytotoxicity test to evaluate its potential biological hazards and proven to manifest relatively high cytotoxicity. This work provides a new fragmentation pattern-based screening strategy for the effective identification of unknown halogenated nucleotides. This method is anticipated to demonstrate broad applications in the nontargeted identification of halogenated nucleotides in diverse environmental samples.
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http://dx.doi.org/10.1016/j.jhazmat.2025.137797 | DOI Listing |
ACS Omega
September 2025
Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510 Ciudad de Mexico, Mexico.
In this study, we introduce a set of novel computational strategies based on second-order Mo̷ller-Plesset perturbation theory (MP2), enhanced through acceleration techniques, such as the resolution of the identity (RI). These approaches are further refined via spin-component scaling (SCS), following Grimme's methodology, and are specifically calibrated for the quantitatively accurate prediction of weak interaction energiesinteractions that play a critical role in biological systems. Among the developed methods, three variants exhibit outstanding performance, surpassing the accuracy of several state-of-the-art, nondynamical electronic structure techniques.
View Article and Find Full Text PDFMolecules
July 2025
State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Rd 40-1, Urumqi 830011, China.
The pyrrolo[2,3-]pyrimidine (7-deazapurine) scaffold is a unique heterocyclic system included in the composition of most nucleotides. In this study, series of the pyrrolo[2,3-]pyrimidine-imines and 3--substituted pyrrolo[2,3-]pyrimidines were designed and prepared in high yields. Condensed pyrimidines are obtained via carbonyl-amine condensation and carbon-halogen bond formation.
View Article and Find Full Text PDFBiochemistry
August 2025
Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan Rd, Chicago, Illinois 60660, United States.
Dihydropyrimidine dehydrogenase from (EcDPD) reduces the 5,6-vinylic bond of pyrimidines using electrons from NADH. Here, we expand on our previous results that demonstrated that EcDPD undergoes reductive activation, that turnover is enhanced in the presence of NADH, and that EcDPD will reoxidize completely in the absence of excess NADH (Alt, T.B.
View Article and Find Full Text PDFACS Infect Dis
August 2025
Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States.
Among several distinct mechanisms used by bacteria to circumvent antibiotic stress, a predominant form of resistance to ribosome-targeting compounds is the methylation of their ribosomal RNA (rRNA) binding sites. The acquisition of aminoglycoside-resistance methyltransferases that modify 16S rRNA nucleotides in the ribosome decoding center, for example, results in exceptionally high-level aminoglycoside resistance and poses a major threat to their future clinical utility. Here, we report the discovery of a first-in-class panel of small-molecule inhibitors that target a previously unexploited composite "Y-shaped" binding pocket that is unique to the 30S subunit (substrate)-bound form of the 16S rRNA (mA1408) methyltransferase NpmA.
View Article and Find Full Text PDFJ Org Chem
July 2025
Department of Chemistry, University of Fribourg, Chemin du Musée 9, Fribourg CH-1700, Switzerland.
Nucleic acid templated reactions are of particular interest for the development of diagnostic tools or the generation of libraries of molecules. Amine/carbonate oligonucleotide templated reactions that release a colored reporter are known, but improvements of performance, in terms of speed, sensitivity, and selectivity, remain necessary. We report here on the synthesis of halogenated arylcarbonates with self-immolative properties that can be readily connected under mild conditions to commercially available alkyne functionalized oligonucleotides using click chemistry.
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