In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular S2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.
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http://dx.doi.org/10.1021/jacs.6b12017 | DOI Listing |
Nat Commun
January 2025
Lab of Low-Dimensional Materials Chemistry, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontier Science Center of the Materials Biology and Dynamic Chemistry, Shanghai Engineering Research Center of Hierarchical Nanomaterials, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, China.
Reactive oxygen species (ROS) is promising in cancer therapy by accelerating tumor cell death, whose therapeutic efficacy, however, is greatly limited by the hypoxia in the tumor microenvironment (TME) and the antioxidant defense. Amplification of oxidative stress has been successfully employed for tumor therapy, but the interactions between cancer cells and the other factors of TME usually lead to inadequate tumor treatments. To tackle this issue, we develop a pH/redox dual-responsive nanomedicine based on the remodeling of cancer-associated fibroblasts (CAFs) for multi-pronged amplification of ROS (ZnPP@FQOS).
View Article and Find Full Text PDFJ Phys Condens Matter
January 2025
Universidade Federal de Santa Maria, Departamento de Física, Santa Maria, RS, 97105-900, BRAZIL.
The study of emerging contaminants (ECs) in water resources has garnered significant attention due to their potential risks to human health and the environment. This review examines the contribution from computational approaches, focusing on the application of machine learning (ML) and molecular dynamics (MD) simulations to understand and optimize experimental applications of ECs adsorption on carbon-based nanomaterials. Condensed matter physics plays a crucial role in this research by investigating the fundamental properties of materials at the atomic and molecular levels, enabling the design and engineering of materials optimized for contaminant removal.
View Article and Find Full Text PDFNat Mater
January 2025
State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
The interconversion between singlet and triplet spin states of photogenerated radical pairs is a genuine quantum process, which can be harnessed to coherently manipulate the recombination products through a magnetic field. This control is central to such diverse fields as molecular optoelectronics, quantum sensing, quantum biology and spin chemistry, but its effect is typically fairly weak in pure molecular systems. Here we introduce hybrid radical pairs constructed from semiconductor quantum dots and organic molecules.
View Article and Find Full Text PDFNeurogenetics
January 2025
Department of Biochemistry, College of Medicine, University of Lagos, Lagos State, Nigeria.
Schizophrenia (SZ) is a complex, chronic mental disorder characterized by positive symptoms (such as delusions and hallucinations), negative symptoms (including anhedonia, alogia, avolition, and social withdrawal), and cognitive deficits (affecting attention, processing speed, verbal and visuospatial learning, problem-solving, working memory, and mental flexibility). Extensive animal and clinical studies have emphasized the NMDAR hypofunction hypothesis of SZ. Glycine plays a crucial role as an agonist of NMDAR, enhancing the receptor's affinity for glutamate and supporting normal synaptic function and plasticity, that is, signal transmission between neurons.
View Article and Find Full Text PDFSci Rep
January 2025
Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
Chemical fungicides have been used to control fungal diseases like Sclerotinia sclerotiorum. These fungicides must be restricted because of their toxicity and the development of resistance strains. Therefore, utilizing natural nanoscale materials in agricultural production is a potential alternative.
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