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Dinitrogen Activation: A Novel Approach with P/B Intermolecular FLP.
J Phys Chem A
January 2025
School of Applied Science and Humanities, Haldia Institute of Technology, ICARE Complex, Haldia 721657, India.
This study explores the reactivity of a new intermolecular P/B frustrated Lewis pair in the context of dinitrogen activation through a push-pull mechanism. The ab initio molecular dynamics model known as atom-centered density matrix propagation plays a pivotal role in elucidating the weakly associated encounter complex. In-depth analysis, mainly through intrinsic reaction coordinate calculations, supports a single-step mechanism.
View Article and Find Full Text PDFGenerative Model for Constructing Reaction Path from Initial to Final States.
J Chem Theory Comput
January 2025
Preferred Networks, Inc., Tokyo 100-0004, Japan.
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths can be difficult for humans. This paper presents an innovative approach that utilizes neural networks to generate initial guesses for reaction pathways based on the initial state and learning from a database of low-energy transition paths.
View Article and Find Full Text PDFNon-metallic iodine single-atom catalysts with optimized electronic structures for efficient Fenton-like reactions.
Nat Commun
January 2025
State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China.
In this study, we introduce a highly effective non-metallic iodine single-atom catalyst (SAC), referred to as I-NC, which is strategically confined within a nitrogen-doped carbon (NC) scaffold. This configuration features a distinctive C-I coordination that optimizes the electronic structure of the nitrogen-adjacent carbon sites. As a result, this arrangement enhances electron transfer from peroxymonosulfate (PMS) to the active sites, particularly the electron-deficient carbon.
View Article and Find Full Text PDFEnhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation.
Nat Commun
January 2025
Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, 851 South Morgan Street, Chicago, IL, 60607, USA.
The bottleneck in enhanced sampling lies in finding collective variables that effectively accelerate protein conformational changes; true reaction coordinates that accurately predict the committor are the well-recognized optimal choice. However, identifying them requires unbiased natural reactive trajectories, which, paradoxically, require effective enhanced sampling. Using the generalized work functional method, we uncover that true reaction coordinates control both conformational changes and energy relaxation, enabling us to compute them from energy relaxation simulations.
View Article and Find Full Text PDFCoordination of inorganic disulfide species to ferric N-acetyl microperoxidase 11.
Biochem Biophys Res Commun
January 2025
Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina. Electronic address:
The interest in chemical interactions between inorganic sulfur species and heme compounds has grown significantly in recent years due to their physiological relevance. The model system ferric N-acetyl microperoxidase 11 (NAcMP11Fe) enables the exploration of the mechanistic aspects of the interaction between the ferric heme group and binding sulfur ligands, without the constraints imposed by a protein matrix and the stabilizing effects of distal amino acids. In this study, we investigated the coordination of disulfane (HSSH) and its conjugate base hydrodisulfide (HSS) to NAcMP11Fe.
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