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It is a well-established standard to describe ground-state chemical reactions at an ab initio level of multi-electron theory. Fast reactions can be directly simulated. The most widely used approach is density functional theory for the electronic structure in combination with molecular dynamics for the nuclear motion. This approach is known as ab initio molecular dynamics. In contrast, the simulation of excited-state reactions at this level of theory is significantly more difficult. It turns out that the self-consistent solution of the Kohn-Sham equations is not easily reached in excited-state simulations. The first program that solved this problem was the Car-Parrinello molecular dynamics code, using restricted open-shell Kohn-Sham theory. Meanwhile, there are alternatives, most prominently the Q-Chem code, which widens the range of applications. The present study investigates the suitability of both codes for the molecular dynamics simulation of excited-state motion and presents applications to photoreactions.
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http://dx.doi.org/10.3390/molecules29184509 | DOI Listing |
Genome Biol
September 2025
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.
Background: Centromeres are crucial for precise chromosome segregation and maintaining genome stability during cell division. However, their evolutionary dynamics, particularly in polyploid organisms with complex genomic architectures, remain largely enigmatic. Allopolyploid wheat, with its well-defined hierarchical ploidy series and recent polyploidization history, serves as an excellent model to explore centromere evolution.
View Article and Find Full Text PDFMol Psychiatry
September 2025
Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Università degli Studi di Milano, Milan, Italy.
Early-life experiences shape neural networks, with heightened plasticity during the so-called "sensitive periods" (SP). SP are regulated by the maturation of GABAergic parvalbumin-positive (PV+) interneurons, which become enwrapped by perineuronal nets (PNNs) over time, modulating SP closure. Additionally, the opening and closing of SP are orchestrated by two distinct gene clusters known as "trigger" and "brake".
View Article and Find Full Text PDFHandb Exp Pharmacol
September 2025
Tsinghua University, Beijing, China.
The μ-opioid receptor (μOR) is the primary drug target of opioid analgesics such as morphine and fentanyl. Activation of μORs in the central nervous system inhibits ascending pain signaling to the cortex, thereby producing analgesic effects. However, the clinical use of opioid analgesics is severely limited by adverse side effects, including respiratory depression, constipation, addiction, and the development of tolerance.
View Article and Find Full Text PDFJ Agric Food Chem
September 2025
College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China.
In the search for novel succinate dehydrogenase inhibitors (SDHIs) fungicides for managing rice sheath blight (RSB) and sclerotinia stem rot (SSR), 28 pyrazole-4-carboxamides incorporating stilbene or diphenylacetylene scaffolds were synthesized and evaluated for antifungal activities. The results showed that compound exhibited the most promising antifungal efficacy against and with EC (half maximal effective concentration) values of 0.004 and 0.
View Article and Find Full Text PDFJ Invertebr Pathol
September 2025
Aquatic and Animal Health Group, CIIMAR, University of Porto, Matosinhos 4450-208, Portugal.
Parasites can induce gene expression changes in their hosts, either benefiting the parasite or the host. In particular, trematodes are not only one of the most ubiquitous groups of aquatic parasites, they also have huge impacts on individual hosts with significant ecological and economic repercussions. The trematode Bucephalus minimus infects Cerastoderma edule (the edible cockle), a socioeconomically and ecologically important bivalve, as its first intermediate host.
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