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CaML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions in calcium-binding proteins using structural and topological features.
Protein Sci
February 2025
Department of Physics, University of Washington, Seattle, Washington, USA.
Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes.
View Article and Find Full Text PDFNovel Insights into Surface Energies and Enhanced Gas-Sensing Capabilities of ZnGaO(111) via Ab Initio Studies.
Sensors (Basel)
January 2025
Graduate Institute of Precision Engineering, National Chung Hsing University, No. 145, Xingda Road, Taichung 40227, Taiwan.
This study investigates the surface energies and work function changes in ZnGaO(111) surfaces with different atomic terminations using ab initio density functional theory. It explores the interactions of gas molecules such as NO, NO, and CHCOCH with Ga-terminated, O-terminated, and Ga-Zn-O-terminated surfaces. This study reveals previously unreported insights into how O-terminated surfaces exhibit enhanced reactivity with NO, resulting in significant work function changes of +6.
View Article and Find Full Text PDFEffect of Inherent Mg/Ti Interface Structure on Element Segregation and Bonding Behavior: An Ab Initio Study.
Materials (Basel)
January 2025
State Key Laboratory of Powder Metallurgy, Central South University, Changsha 410083, China.
To provide insight into the interface structure in Ti particle-reinforced Mg matrix composites, this study investigates the inherent Mg/Ti interface structure formed during the solidification of supercooled Mg melt on a (0001)Ti substrate using ab initio molecular dynamics (AIMD) simulations and density function theory (DFT) calculation. The resulting interface exhibits an orientation relationship of 0001Mg//0001Ti with a lattice mismatch of approximately 8%. Detailed characterizations reveal the occurrences of 0001Mg plane rotation and vacancy formation to overcome the lattice mismatch at the inherent Mg/Ti interface while allowing Mg atoms to occupy the energetically favorable hollow sites above the Ti atomic layer.
View Article and Find Full Text PDFNearly Barrierless Four-Hole Water Oxidation Catalysis on Semiconductor Photoanodes with High Density of Accumulated Surface Holes.
J Am Chem Soc
January 2025
Key Laboratory of Photochemistry, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
The sluggish water oxidation reaction (WOR) is considered the kinetic bottleneck of artificial photosynthesis due to the complicated four-electron and four-proton transfer process. Herein, we find that the WOR can be kinetically nearly barrierless on four representative photoanodes (i.e.
View Article and Find Full Text PDFRevealing the catalytic oxidation mechanism of CO on α-FeO surfaces: an thermodynamic study.
Phys Chem Chem Phys
January 2025
Institute of Nanomaterials, Faculty of Materials Science, Kim Il Sung University, Ryongnam-Dong, Taesong District, Pyongyang, Democratic People's Republic of Korea.
Significant research efforts have been devoted to improving the efficiency of catalytic carbon monoxide (CO) oxidation over α-FeO-based catalysts, but details of the underlying mechanism are still under debate. Here we apply the thermodynamic method (AITM) within the density functional theory framework to investigate the phase diagram of α-FeO(0001) surfaces with various terminations and the catalytic mechanism of CO oxidation on these surfaces. By extending the conventional AITM to consider the charge state of surface defects, we build the phase diagram of α-FeO(0001) surfaces in relation to the Fermi energy as well as the oxygen chemical potential, which makes it possible to explain the influence of point defects on the surface morphology and to predict the existence of the experimentally observed functional sites such as the ferryl group (FeO) and oxygen vacancies.
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