Anharmonic calculations using vibrational perturbation theory are known to provide near-spectroscopic accuracy when combined with high-level ab initio potential energy functions. However, performance with economical, popular electronic structure methods is less well characterized. We compare the accuracy of harmonic and anharmonic predictions from Hartree-Fock, second-order perturbation, and density functional theories combined with 6-31G(d) and 6-31+G(d,p) basis sets. As expected, anharmonic frequencies are closer than harmonic frequencies to experimental fundamentals. However, common practice is to correct harmonic predictions using multiplicative scaling. The surprising conclusion is that scaled anharmonic calculations are no more accurate than scaled harmonic calculations for the basis sets we used. The data used are from the Computational Chemistry Comparison and Benchmark Database (CCCBDB), maintained by the National Institute of Standards and Technology, which includes more than 3939 independent vibrations for 358 molecules.
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http://dx.doi.org/10.1021/ct300293a | DOI Listing |
J Immunother Cancer
January 2025
National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, China
Background: Clear cell renal cell carcinoma (ccRCC) is the most common histologic type of RCC. However, the spatial and functional heterogeneity of immunosuppressive cells and the mechanisms by which their interactions promote immunosuppression in the ccRCC have not been thoroughly investigated.
Methods: To further investigate the cellular and regional heterogeneity of ccRCC, we analyzed single-cell and spatial transcriptome RNA sequencing data from four patients, which were obtained from samples from multiple regions, including the tumor core, tumor-normal interface, and distal normal tissue.
J Comput Chem
January 2025
Universidade de São Paulo, Instituto de Química, Departamento de Química Fundamental, São Paulo, Brazil.
Seventeen electronic states of the dication VH were characterized by the SA-CASSCF/icMRCI methodology using very extended basis sets; 11 were described for the first time. Potential energy curves were constructed and the associated spectroscopic parameters evaluated. Triplet and quintet states correlating with the V + H channel are thermodynamic stable.
View Article and Find Full Text PDFJ Mol Model
January 2025
Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
Context: The analysis of the changes in the electronic structure along intrinsic reaction coordinate (IRC) paths for model reactions: (i) ethylene + butadiene cycloaddition, (ii) prototype SN2 reaction Cl + CH3Cl, (iii) HCN/CNH isomerization assisted by water, (iv) CO + HF → C(O)HF was performed, in terms of changes in the deformation density (Δr) and the deformation of MEP (ΔMEP). The main goal was to further examine the utility of the ΔMEP as a descriptor of chemical bonding, and to compare the pictures resulting from Δr and ΔMEP. Both approaches clearly show that the main changes in the electronic structure occur in the TS region.
View Article and Find Full Text PDFDrug Dev Res
February 2025
Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
Familial encephalopathy with neuroserpin inclusion bodies (FENIB) is a neurodegenerative pathology caused by accumulation of mutant neuroserpin (NS) polymers inside the endoplasmic reticulum (ER) of neurons, leading to cellular toxicity and neuronal death. To date, there is no cure for FENIB, and only palliative care is available for FENIB patients, underlining the urgency to develop therapeutic strategies. The purpose of this work was to create a cellular system designed for testing small molecules able to reduce the formation of NS polymers.
View Article and Find Full Text PDFSci Rep
January 2025
Faculty of Education and Arts, Australian Catholic University, Sydney, NSW, 2118, Australia.
Every node in a network is said to be resolved if it can be uniquely identified by a vector of distances to a specific set of nodes. The metric dimension is equivalent to the least possible cardinal number of a resolving set. Conditional resolving sets are obtained by imposing various constraints on resolving set.
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