Here we explored the performance of Hartree-Fock (HF), Perdew-Burke-Ernzerhof (PBE), and Tao-Perdew-Staroverov-Scuseria (TPSS) functionals in predicting core level 1s binding energies (BEs) and BE shifts (ΔBEs) for a large set of 68 molecules containing a wide variety of functional groups for main group elements B → F and considering up to 185 core levels. A statistical analysis comparing with X-ray photoelectron spectroscopy (XPS) experiments shows that BEs estimations are very accurate, TPSS exhibiting the best performance. Considering ΔBEs, the three methods yield very similar and excellent results, with mean absolute deviations of ∼0.25 eV. When considering relativistic effects, BEs deviations drop approaching experimental values. So, the largest mean percentage deviation is of 0.25% only. Linear trends among experimental and estimated values have been found, gaining offsets with respect to ideality. By adding relativistic effects to offsets, HF and TPSS methods underestimate experimental values by solely 0.11 and 0.05 eV, respectively, well within XPS chemical precision. TPSS is posed as an excellent choice for the characterization, by XPS, of molecules on metal solid substrates, given its suitability in describing metal substrates bonds and atomic and/or molecular orbitals.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jctc.5b00998 | DOI Listing |
J Cheminform
January 2025
Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK.
Current strategies centred on either merging or linking initial hits from fragment-based drug design (FBDD) crystallographic screens generally do not fully leaverage 3D structural information. We show that an algorithmic approach (Fragmenstein) that 'stitches' the ligand atoms from this structural information together can provide more accurate and reliable predictions for protein-ligand complex conformation than general methods such as pharmacophore-constrained docking. This approach works under the assumption of conserved binding: when a larger molecule is designed containing the initial fragment hit, the common substructure between the two will adopt the same binding mode.
View Article and Find Full Text PDFMol Autism
January 2025
Department of Special Education, University of Haifa, Haifa, Israel.
Background: Alterations in sensory perception, a core phenotype of autism, are attributed to imbalanced integration of sensory information and prior knowledge during perceptual statistical (Bayesian) inference. This hypothesis has gained momentum in recent years, partly because it can be implemented both at the computational level, as in Bayesian perception, and at the level of canonical neural microcircuitry, as in predictive coding. However, empirical investigations have yielded conflicting results with evidence remaining limited.
View Article and Find Full Text PDFZhongguo Zhong Yao Za Zhi
December 2024
Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China.
This study aimed to investigate the potential role of Colquhounia Root Tablets against bone destruction in rheumatoid arthritis(RA) and its molecular mechanism. The study used ultra-performance liquid chromatography-mass spectrometry to analyze the major components of Colquhounia Root Tablets and predicted its candidate target gene set based on the major components. The key targets of RA bone destruction were obtained through GeneCards and the Database of Genetics and Medical Literature(OMIM), protein-protein interaction(PPI) network was constructed, and the key targets were identified by topological analysis.
View Article and Find Full Text PDFNeurobiol Dis
January 2025
Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, Guangxi, China. Electronic address:
One of the underlying mechanisms of epilepsy (EP), a brain disease characterized by recurrent seizures, is considered to be cell death. Disulfidptosis, a proposed novel cell death mechanism, is thought to play a part in the pathogenesis of epilepsy, but the exact role is unclear. The gene expression omnibus series (GSE) 33,000 and GSE63808 datasets were used to search for differentially expressed disulfidptosis-related molecules (DE-DRMs).
View Article and Find Full Text PDFAcc Chem Res
January 2025
Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.
ConspectusReactions of gas phase molecules with surfaces play key roles in atmospheric and environmental chemistry. Reactive uptake coefficients (γ), the fraction of gas-surface collisions that yield a reaction, are used to quantify the kinetics in these heterogeneous and multiphase systems. Unlike rate coefficients for homogeneous gas- or liquid-phase reactions, uptake coefficients are system- and observation-dependent quantities that depend upon a multitude of underlying elementary steps.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!