The magnitude of intramolecular basis set superposition error (BSSE) is revealed via computing systematic trends in molecular properties. This type of error is largely neglected in the study of the chemical properties of small molecules and it has historically been analyzed just in the study of large molecules and processes dominated by non-covalent interactions (typically dimerization or molecular complexation and recognition events). In this work we try to provide proof of the broader prevalence of this error, which permeates all types of electronic structure calculations, particularly when employing insufficiently large basis sets.
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http://dx.doi.org/10.3390/molecules24203810 | DOI Listing |
J Chem Theory Comput
January 2025
Qingdao Institute for Theoretical and Computational Sciences and Center for Optics Research and Engineering, Shandong University, Qingdao 266237, China.
Given a number of data sets for evaluating the performance of single reference methods for the low-lying excited states of closed-shell molecules, a comprehensive data set for assessing the performance of multireference methods for the low-lying excited states of open-shell systems is still lacking. For this reason, we propose an extension (QUEST#4X) of the radical subset of QUEST#4 ( , , 3720) to cover 110 doublet and 39 quartet excited states. Near-exact results obtained by iterative configuration interaction with selection and second-order perturbation correction (iCIPT2) are taken as benchmark to calibrate static-dynamic-static configuration interaction (SDSCI) and static-dynamic-static second-order perturbation theory (SDSPT2), which are minimal MRCI and CI-like perturbation theory, respectively.
View Article and Find Full Text PDFAnnu Rev Entomol
January 2025
Department of Entomology, China Agricultural University, Beijing, China; email:
Thanks to the fast development of sequencing techniques and bioinformatics tools, sequencing the genome of an insect species for specific research purposes has become an increasingly popular practice. Insect genomes not only provide sets of gene sequences but also represent a change in focus from reductionism to systemic biology in the field of entomology. Using insect genomes, researchers are able to identify and study the functions of all members of a gene family, pathway, or gene network associated with a trait of interest.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromso̷ N-9037, Norway.
We introduce a method for computing quantum mechanical forces through surface integrals over the stress tensor within the framework of the density functional theory. This approach avoids the inaccuracies of traditional force calculations using the Hellmann-Feynman theorem when applied to multiresolution wavelet representations of orbitals. By integrating the quantum mechanical stress tensor over surfaces that enclose individual nuclei, we achieve highly accurate forces that exhibit superior consistency with the potential energy surface.
View Article and Find Full Text PDFJ Alzheimers Dis
January 2025
Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Background: Endogenous Alu RNAs form double-stranded RNAs recognized by double-stranded RNA sensors and activate IRF and NF-kB transcriptional paths and innate immunity. Deamination of adenosines to inosines by the ADAR family of enzymes, a process termed A-to-I editing, disrupts double-stranded RNA structure and prevents innate immune activation. Innate immune activation is observed in Alzheimer's disease, the most common form of dementia.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Urology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, People's Republic of China.
Benign prostatic hyperplasia (BPH) is a prevalent urinary system disorder. Despite evidence of a significant genetic component from previous studies, the specific pathogenic genes and biological mechanisms are still largely unknown. The study utilized the FinnGen R10 dataset, encompassing 177,901 individuals (36,601 cases and 141,300 controls), and the GTEx v8 EQTLs files to conduct single-tissue and cross-tissue transcriptome-wide association studies (TWAS).
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