98%
921
2 minutes
20
The prevailing reactive force fields are typically based on the bond-order concept or other predefined chemical frameworks, along with implicit electronic treatments and the incorporation of intricate corrections, which severely limit their further development. Explicit electron force fields introduce electrons as particles into the force field, and their ability to model electronically excited systems as well as electronic response properties has been demonstrated, yet the description of ground-state reactions for complex systems remains challenging. This study introduces a new explicit electron force field (EeFF) for modeling hydrocarbon ground-state reactions. The EeFF explicitly treats electrons as distinct wave packets with variable radii and variable spin properties, thus providing a more physically realistic description of electronic behavior. The model incorporates quantum kinetic energy, Coulomb integration, and Pauli repulsion of electrons by introducing specialized potential functions applicable to different types of wave packets, thereby superseding the traditional bond-order concept. The EeFF has been optimized using training sets of CH compounds with more than 10000 conformations covering a wide range of hydrocarbon systems and reactions. Compared with ReaxFF, EeFF reduces energy and force errors. A new molecular dynamics simulation method is used to realize the dynamic evolution of electron spin properties and allow the degrees of freedom of nuclei and electrons to change over time while approaching adiabatic conditions. Subsequent simulations of iso-octane thermal decomposition effectively reproduce the main product distributions as well as the key reaction pathways, and the motion trajectories of electrons provide unique insights into the reaction mechanisms at the electron level.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jctc.5c00633 | DOI Listing |
Free Radic Biol Med
September 2025
Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, The First Affiliated Hospital of Guangxi Medical, University, Nanning, Guangxi, 530021, China; Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Educatio
Background: The second most common cause of autosomal recessive early-onset Parkinson's disease (PD) can be attributed to mutations in the PINK1 gene, malfunction of the mitochondria is the key pathological mechanism. Bre1 encodes an E3 ubiquitin ligase, with the discovery of Bre1's role in repairing mitochondrial damage, further investigation into its implications for PD is warranted.
Methods: We used the PINK1 drosophila melanogaster as the PD model.
J Am Soc Mass Spectrom
September 2025
Mulliken Center for Theoretical Chemistry, Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
Collision-induced dissociation mass spectrometry (CID-MS) is an important tool in analytical chemistry for the structural elucidation of unknown compounds. The theoretical prediction of the CID spectra plays a critical role in supporting and accelerating this process. To this end, we adapt the recently developed QCxMS2 program originally designed for the calculation of electron ionization (EI) spectra to enable the computation of CID-MS.
View Article and Find Full Text PDFJ Phys Chem A
September 2025
Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1-5, Rue de la Doua, F-69100 Villeurbanne, France.
We introduce a variational formulation of nucleophilicity within the framework of conceptual density functional theory (CDFT), thus proposing a maximum nucleophilicity principle (MNP), in formal analogy to the established minimum electrophilicity principle (MEP). Starting from a third-order Taylor expansion of the electronic energy with respect to the number of electrons at constant external potential, we extend our recently proposed global nucleophilicity index derived from the chemical potential μ, hardness η, and hyperhardness γ. We demonstrate that this index follows a well-defined variational condition for electron-loss processes.
View Article and Find Full Text PDFMol Biol Rep
September 2025
Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
Background: Colorectal cancer (CRC) is one of the most common cancers worldwide and is often treated with chemotherapy. However, systemic toxicity, non-specificity, and drug resistance are major challenges associated with chemotherapeutic drugs. Nanocarriers such as niosomes (NIOs) can enhance drug accumulation at the tumor site while minimizing systemic side effects.
View Article and Find Full Text PDFJ Phys Chem B
August 2025
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zürich, ZH 8057, Switzerland.
The tau protein is a major component of neurofibrillary tangles, one of the hallmarks of Alzheimer's disease, which is the most common neurodegenerative disorder in the elderly. Experimental and computational studies have shed light on the fibrillar morphologies of tau and the kinetics of self-assembly, but little is known about the structural stability of the fibrils in the presence of external electric fields. We investigated the behavior of cross-β filaments of tau under the effect of an oscillating external electric field by means of multiple molecular dynamics simulations.
View Article and Find Full Text PDF