The O(2) and NO reactivity of a Cr(II) complex bearing a 12-membered tetraazamacrocyclic N-tetramethylated cyclam (TMC) ligand, [Cr(II)(12-TMC)(Cl)](+) (1), and the NO reactivity of its peroxo derivative, [Cr(IV)(12-TMC)(O(2))(Cl)](+) (2), are described. By contrast to the previously reported Cr(III)-superoxo complex, [Cr(III)(14-TMC)(O(2))(Cl)](+), the Cr(IV)-peroxo complex 2 is formed in the reaction of 1 and O(2). Full spectroscopic and X-ray analysis revealed that 2 possesses side-on η(2)-peroxo ligation. The quantitative reaction of 2 with NO affords a reduction in Cr oxidation state, producing a Cr(III)-nitrato complex, [Cr(III)(12-TMC)(NO(3))(Cl)](+) (3). The latter is suggested to form via a Cr(III)-peroxynitrite intermediate. [Cr(II)(12-TMC)(NO)(Cl)](+) (4), a Cr(II)-nitrosyl complex derived from 1 and NO, could also be synthesized; however, it does not react with O(2).
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http://dx.doi.org/10.1021/ja307384e | DOI Listing |
G3 (Bethesda)
January 2025
School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA.
The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection.
View Article and Find Full Text PDFBrief Bioinform
November 2024
School of Computer Science, Northwestern Polytechnical University, Xi'an, 710129 Shaanxi, China.
The identification of neoantigens is crucial for advancing vaccines, diagnostics, and immunotherapies. Despite this importance, a fundamental question remains: how to model the presentation of neoantigens by major histocompatibility complex class I molecules and the recognition of the peptide-MHC-I (pMHC-I) complex by T cell receptors (TCRs). Accurate prediction of pMHC-I binding and TCR recognition remains a significant computational challenge in immunology due to intricate binding motifs and the long-tail distribution of known binding pairs in public databases.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, 999077, China.
The complexity of T cell receptor (TCR) sequences, particularly within the complementarity-determining region 3 (CDR3), requires efficient embedding methods for applying machine learning to immunology. While various TCR CDR3 embedding strategies have been proposed, the absence of their systematic evaluations created perplexity in the community. Here, we extracted CDR3 embedding models from 19 existing methods and benchmarked these models with four curated datasets by accessing their impact on the performance of TCR downstream tasks, including TCR-epitope binding affinity prediction, epitope-specific TCR identification, TCR clustering, and visualization analysis.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States.
Hydrogen atom transfer (HAT) reactions and their kinetic barriers Δ are important in organic and inorganic chemistry. This study examines factors that influence Δ, reporting the kinetics and thermodynamics of HAT from various ruthenium bis(acetylacetonate) pyridine-imidazole complexes to nitroxyl radicals. Across these 36 reactions, the Δ and Δ can be independently varied, with different sets of Ru complexes primarily tuning either their ps or their °s.
View Article and Find Full Text PDFDalton Trans
January 2025
CEQUINOR (UNLP, CCT-CONICET La Plata, asociado a CIC), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Blvd. 120 No. 1465, La Plata (1900), Argentina.
In this work, we evaluated the anticancer activity of compounds 1 (mononuclear) and 2 (dinuclear) copper(II) coordination compounds derived from the ligand 5-methylsalicylaldehyde 2-furoyl hydrazone (H2L) over MDA-MB-231 Triple-negative breast cancer (TNBC) cells, and compared their activities with that of a newly synthesized, protonated, dinuclear analogue of 2 (complex 3). Here, we report the synthesis of compound 3 and it has been characterized in the solid state (X-ray diffraction, FTIR) and in solution (EPR, UV-Vis, ESI) as well as its electrochemical profile. Complexes 1-3 impaired cell viability from 0.
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