The acid dissociation (ionization) constant pK(a) is one of the fundamental properties of organic molecules. We have evaluated different computational strategies and models to predict the pK(a) values of substituted phenols using partial atomic charges. Partial atomic charges for 124 phenol molecules were calculated using 83 approaches containing seven theory levels (MP2, HF, B3LYP, BLYP, BP86, AM1, and PM3), three basis sets (6-31G*, 6-311G, STO-3G), and five population analyses (MPA, NPA, Hirshfeld, MK, and Löwdin). The correlations between pK(a) and various atomic charge descriptors were examined, and the best descriptors were selected for preparing the quantitative structure-property relationship (QSPR) models. One QSPR model was created for each of the 83 approaches to charge calculation, and then the accuracy of all these models was analyzed and compared. The pK(a)s predicted by most of the models correlate strongly with experimental pK(a) values. For example, more than 25% of the models have correlation coefficients (R²) greater than 0.95 and root-mean-square errors smaller than 0.49. All seven examined theory levels are applicable for pK(a) prediction from charges. The best results were obtained for the MP2 and HF level of theory. The most suitable basis set was found to be 6-31G*. The 6-311G basis set provided slightly weaker correlations, and unexpectedly also, the STO-3G basis set is applicable for the QSPR modeling of pK(a). The Mulliken, natural, and Löwdin population analyses provide accurate models for all tested theory levels and basis sets. The results provided by the Hirshfeld population analysis were also acceptable, but the QSPR models based on MK charges show only weak correlations.
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http://dx.doi.org/10.1021/ci200133w | DOI Listing |
J Steroid Biochem Mol Biol
December 2024
Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China. Electronic address:
Curcuminoids, including curcumin and its derivatives, show potent inhibition of aromatase (CYP19A1), crucial for estradiol synthesis and breast cancer metastasis. Our study evaluated the efficacy and mechanism of 10 curcuminoids and their metabolites against human and rat CYP19A1 using placental microsomes, revealing species-specific IC values. Cyclocurcumin (IC, 4.
View Article and Find Full Text PDFFront Physiol
December 2024
National Heart and Lung Institute, Imperial College London, London, United Kingdom.
Introduction: Adrenergic activation of protein kinase A (PKA) in cardiac muscle targets the sarcolemma, sarcoplasmic reticulum, and contractile apparatus to increase contractile force and heart rate. In the thin filaments of the contractile apparatus, cardiac troponin I (cTnI) Ser22 and Ser23 in the cardiac-specific N-terminal peptide (NcTnI: residues 1 to 32) are the targets for PKA phosphorylation. Phosphorylation causes a 2-3 fold decrease of affinity of cTn for Ca associated with a higher rate of Ca dissociation from cTnC leading to a faster relaxation rate of the cardiac muscle (lusitropy).
View Article and Find Full Text PDFToxins (Basel)
December 2024
All-Russian Research Institute of Phytopathology of RAS, Bolshie Vyazemy, 143050 Moscow, Russia.
An acidic shift in the pH profile of zearalenone hydrolase (ZHD), the most effective and well-studied zearalenone-specific lactone hydrolase, is required to extend the range of applications for the enzyme as a decontamination agent in the feed and food production industries. Amino acid substitutions were engineered in the active center of the enzyme to decrease the pKa values of the catalytic residues E126 and H242. The T216K substitution provided a shift in the pH optimum by one unit to the acidic region, accompanied by a notable expansion in the pH profile under acidic conditions.
View Article and Find Full Text PDFEur J Radiol
December 2024
The Health Information and Quality Authority (HIQA), Unit 1301, City Gate, Mahon, Cork, T12 Y2xt Cork, Ireland. Electronic address:
Purpose: The purpose of this work was to establish national Irish diagnostic reference levels (DRLs) for a clinically representative and comprehensive list of clinical indications, anatomical regions, and common procedures for fluoroscopy and fluoroscopically guided interventions and compare these, where possible, to other DRLs established at a national level.
Method: A list of clinical indications, anatomical regions and common procedures was established. A national database of service providers was used to identify all medical radiological facilities providing fluoroscopy and fluoroscopically guided intervention services.
bioRxiv
December 2024
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
Machine learning has emerged as a promising approach for predicting molecular properties of proteins, as it addresses limitations of experimental and traditional computational methods. Here, we introduce GSnet, a graph neural network (GNN) trained to predict physicochemical and geometric properties including solvation free energies, diffusion constants, and hydrodynamic radii, based on three-dimensional protein structures. By leveraging transfer learning, pre-trained GSnet embeddings were adapted to predict solvent-accessible surface area (SASA) and residue-specific p values, achieving high accuracy and generalizability.
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