In this Letter, we report the first observation of the capacitance-potential hysteresis at the ionic liquid vertical bar electrode interface in atomistic molecular dynamics simulations. While modeling the differential capacitance dependence on the potential scan direction, we detected two long-living types of interfacial structure for the BMImPF(6) ionic liquid at specific charge densities of the gold Au(111) surface. These structures differ in how counterions overscreen the surface charge. The high barrier for the transition from one structure to another slows down the interfacial restructuring process and leads to the marked capacitance-potential hysteresis.

A huge amount of chemical and biological data that is available in several online databases can now be easily retrieved and studied by many researchers (including QSAR modelers) to extract meaningful information. Everyone is naturally aware, however, of the errors in chemical structures and biological data that are possibly present in the retrieved data from these online databases. Implications of those might be severe, particularly for QSAR modelers since developing models using such erroneous data will certainly lead to false or non-predictive models. Proper curation of the retrieved chemical and biological data is therefore crucial and mandatory prior to any QSAR modeling. For large datasets, manual data curation becomes highly impossible, nevertheless. This chapter reviews and discusses the several data curation tools normally applied for such endeavors, paying special attention to those that can be used to semiautomate the curation process, like resorting to a workflow by employing the freely available KNIME software. © Springer Science+Business Media, LLC, part of Springer Nature 2020.

Coumarin phytoestrogens, as one of the important classes of phytoestrogens, have been proved to play an important role in various fields of human life. In this study, molecular simulation method including molecular docking and molecular dynamics methods were performed to explore the various effects between four classical coumarin phytoestrogens (coumestrol, 4-methoxycoumestrol, psoralen and isopsoralen), and estrogen receptors (ER alpha, ER beta), respectively. The calculated results not only proved that the four coumarin phytoestrogens have weaker affinity than 17 beta -estradiol to both ER alpha, and ER beta, but also pointed out that the selective affinity for ER beta is greater than ER alpha. In addition, the binding mode indicated that the formation of hydrogen bond and hydrophobic interaction have an important effect on the stability of the complexes. Further, the calculation and decomposition of binding free energy explored the main contribution interactions to the total free energy.

This chapter will focus on the perception of scientific topics throughout digital dissemination and educational activities. By assessing the evolution on the impact of massive online information dissemination in scientific topics, the chapter aims to address the issue of quality and reliability of scientific information, disseminated towards university students. For this assessment, it will be argued if we must be concerned about a new generation of students being (intentionally or not) misinformed about core insights of their development. This will be done by outlining the major influences of digital and social media in science students ' scholastic activities. By adapting scientific models on the spread of misinformation, this chapter argues how students can be subject to gather and to be exposed to unfiltered data, which can potentially be demeaning to their educational development. © 2021 by IGI Global. All rights reserved.

Three-dimensional conformational crystallographic binding-modes are of paramount importance to understand the docking mechanism of protein-ligand interactions and to identify potential "leading drugs" conformers towards rational drugs-design. Herein, we present an integrated computational-experimental study tackling the problem of multiple binding modes among the ligand 3-(2-Benzothiazolylthio)-propane sulfonic acid (BTS) and the fibrinogen receptor (E-region). Based on molecular docking simulations, we found that the free energy of binding values for nine of different BTS-docking complexes (i.e., BTS-pose_1-9) were very close. We have also identified a docking-mechanismof BTS-interactionmainly based on non-covalent hydrophobic interactions with H-bond contacts stabilizing the fibrinogen-BTS docking complexes. Interestingly, the different BTS-poses_1-9 were found to be able to block the fibrinogen binding site (E-region) by inducing local perturbations in effector and allosteric residues, reducing the degree of collectivity in its flexibility normal modes. As such, wetheoretically suggest that the BTS-bindingmodes can significantly affect the physiological condition of the unoccupied fibrinogen protein structure by bringing global and local perturbations in the frequency domain spectra. The proposed theoretical mechanisms, the interactions involved and the conformational changes suggested, were further corroborated by different experimental techniques such as isothermal titration calorimetry (ITC), zeta potential, UV-vis, fluorescence and small angle X-ray scattering (SAXS). The combined results shall open new avenues towards the application of complex supra-molecular information in rational drugs-design.

[No abstract available]

<jats:sec> <jats:title /> <jats:p /> </jats:sec>

<jats:p>Herein, we present a combination of experimental and computational study on the mitochondrial F0F1-ATPase nanotoxicity inhibition induced by single-walled carbon nanotubes (SWCNT-pristine, SWCNT-COOH). To this end, the in vitro inhibition responses in submitochondrial particles (SMP) as F0F1-ATPase enzyme were strongly dependent on the concentration assay (from 3 to 5 &amp;micro;g/ml) for both types of carbon nanotubes. Besides, both SWCNTs show an interaction inhibition pattern like the oligomycin A (the specific mitochondria F0F1-ATPase inhibitor). Furthermore, the best crystallography binding pose obtained for the docking complexes based on the free energy of binding (FEB), fit well with the previous in vitro evidences from the thermodynamics point of view. Following an affinity order as: FEB (oligomycin A/F0-ATPase complex) = -9.8 kcal/mol &amp;gt; FEB (SWCNT-COOH/F0-ATPase complex) = - 6.8 kcal/mol ~ FEB (SWCNT-pristine complex) = -5.9 kcal/mol. With predominance of van der Waals hydrophobic nanointeractions with key F0-ATPase binding site residues (Phe 55 and Phe 64). By the other hand, results on elastic network models, and fractal-surface analysis suggest that SWCNTs induce significant perturbations by triggering abnormal allosteric responses and signals propagation in the inter-residue network which could affect the substrate recognition ligand geometrical specificity of the F0F1-ATPase enzyme in order (SWCNT-pristine &amp;gt; SWCNT-COOH). Besides, the performed Nano-QSTR models for both SWCNTs show that this method may be used for the prediction of the nanotoxicity induced by SWCNT. Overall, the obtained results may open new avenues toward to the better understanding and prediction of new nanotoxicity mechanisms, rational drug-design based nanotechnology, and potential biomedical application in precision nanomedicine.</jats:p>