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Tetrahedral AlO Cage: A Superchalcogen Atom.
J Phys Chem A
January 2025
School of Chemistry & Chemical Engineering, Anhui University, Hefei, Anhui 230601, PR China.
Superatoms are stable clusters that mimic the chemical behavior of individual atoms in the periodic table. Many endeavors have been devoted to the design and characterization of various superatoms, while engineering superatoms to mimic the chemistry of chalcogens remains a challenge. In this paper, we present a new superchalcogen by evaluating a hollow tetrahedral AlO cluster with theoretical calculations.
View Article and Find Full Text PDFGermanium Atoms Exceed the Tetrahedral Coordination in MFI Zeolite.
J Am Chem Soc
January 2025
Université de Caen Normandie, ENSICAEN, CNRS, LCS, 14000 Caen, France.
Germanium is known to occupy tetrahedral sites by substituting silicon in germanosilicate zeolites. In this study, we present pioneering findings regarding the synthesis of zeolites with an MFI structure (GeMFI) incorporating a high germanium amount (16% Ge). Remarkably, the germanium atoms feature a slight electron deficiency with respect to GeO, and the typical coordination number of 4, as usually reported for the germanosilicate zeolites, is exceeded, giving rise to Ge dimers in a double-bridge configuration.
View Article and Find Full Text PDFSimultaneous sensitive detection and imaging of dual microRNAs through DNA tetrahedral scaffold-corbelled autonomous-motion molecular machine.
Talanta
January 2025
School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China.
Sensitive and accurate detection and imaging of different microRNAs (miRNAs) in cancer cells hold great promise for early disease diagnosis. Herein, a DNA tetrahedral scaffold (DTS)-corbelled autonomous-motion (AM) molecular machine based fluorescent sensing platform was designed for simultaneous detection of two types of miRNAs (miRNA-21 and miRNA-155) in HeLa cells. Locking-strand-silenced DNAzymes (P:L duplex) were firstly grafted at the loop of target-analogue-embedded double-stem hairpin substrates (TDHS) of DTS, making the sensor in a "signal off" state due to the closely distance between modified fluorophores (FAM and Cy5) with the corresponding quenchers (BHQ1 and BHQ2).
View Article and Find Full Text PDFActivation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations.
J Chem Inf Model
January 2025
Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
Cezanne-2 (Cez2) is a deubiquitinylating (DUB) enzyme involved in the regulation of ubiquitin-driven cellular signaling and selectively targets Lys11-linked polyubiquitin chains. As a representative member of the ovarian tumor (OTU) subfamily DUBs, it performs cysteine proteolytic isopeptide bond cleavage; however, its exact catalytic mechanism is not yet resolved. In this work, we used different computational approaches to get molecular insights into the Cezanne-2 catalytic mechanism.
View Article and Find Full Text PDFComputational Study on the Reaction Mechanism of 5-Enolpyruvylshikimate-3-phosphate Synthase from Nicotiana Tabacum.
ChemistryOpen
January 2025
Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the conversion of 5-enolpyruvate (PEP) and shikimic acid phosphate (S3P) to 5-enolpyruvylshikimic acid-3-phosphate (EPSP), releasing inorganic phosphate. This reaction is the sixth step of the shikimate pathway, which is a metabolic pathway used by microorganisms and plants for the biosynthesis of aromatic amino acids and folates but not in mammals. In the present study, the detailed reaction mechanism of EPSPS from Nicotiana tabacum (NtEPSPS) is revealed by quantum chemical calculations with the cluster approach.
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