In Silico Inhibitability of Copper Carbenes and Silylenes against Rhizoctonia solani and Magnaporthe oryzae

Copper lighter tetrylenes are promising for inhibition towards Rhizoctonia solani-based protein PDB-4G9M and Magnaporthe oryzae-based PDB-6JBR in rice. Quantum properties of four hypothetic copper complexes of carbenes and silylenes (Cu-NHC1, Cu-NHC2, Cu-NHSi1, and Cu-NHSi2) were examined using the density functional theory. Their inhibitability towards the targeted proteins was evaluated using molecular docking simulation. Quantum analysis predicts the stability of the investigated complexes and thus their practical existability and practicable synthesisability. Their electronic configurations are justified as highly conducive to intermolecular interaction. Regarding ligand-protein as carbenes/silylenes-4G9M inhibitory structures, the stability is estimated in the order [Cu-NHC2]-4G9M (DS −12.9 kcal⋅mol−1) > [Cu-NHSi1]-4G9M (DS −11.8 kcal⋅mol−1) = [Cu-NHSi2]-4G9M (DS −11.7 kcal⋅mol−1) > [Cu-NHC1]-4G9M (DS –11.4 kcal⋅mol−1). In contrast, the corresponding order for the carbenes/silylenes-6JBR systems is [Cu-NHSi2]-6JBR (DS –13.4 kcal⋅mol−1) > [Cu-NHC2]-6JBR (DS −13.0 kcal⋅mol−1) = [Cu-NHSi1]-6JBR (DS −12.6 kcal⋅mol−1) > [Cu-NHC1]-6JBR (DS −12.3 kcal⋅mol−1). In theory, this study suggests a potentiality of copper lighter tetrylenes and their derivatives against the infection of fungi Rhizoctonia solani and Magnaporthe oryzae, thus encouraging attempts for experimental developments.

Computational repurposing of benzimidazole anthelmintic drugs as potential colchicine binding site inhibitors

Background: Although some benzimidazole-based anthelmintic drugs are found to possess anticancer activity, their modes of binding interactions have not been reported. Methodology: In this study, we aimed to investigate the binding interactions and electronic configurations of nine benzimidazole-based anthelmintics against one of the well-known cancer targets (tubulin protein). Results: Binding affinities of docked benzimidazole drugs into colchicine-binding site were calculated where flubendazole > oxfendazole > nocodazole > mebendazole. Flubendazole was found to bind more efficiently with tubulin protein than other drugs. Quantum mechanics studies revealed that the electron density of HOMO of flubendazole and mebendazole together with their molecular electrostatic potential map are closely similar to that of nocodazole. Conclusion: Our study has ramifications for considering repurposing of flubendazole as a promising anticancer candidate.

Characterization of Charge States in Conducting Organic Nanoparticles by X-ray Photoemission Spectroscopy

The metallic and semiconducting character of a large family of organic materials based on the electron donor molecule tetrathiafulvalene (TTF) is rooted in the partial oxidation (charge transfer or mixed valency) of TTF derivatives leading to partially filled molecular orbital-based electronic bands. The intrinsic structure of such complexes, with segregated donor and acceptor molecular chains or planes, leads to anisotropic electronic properties (quasi one-dimensional or two-dimensional) and morphology (needle-like or platelet-like crystals). Recently, such materials have been synthesized as nanoparticles by intentionally frustrating the intrinsic anisotropic growth. X-ray photoemission spectroscopy (XPS) has emerged as a valuable technique to characterize the transfer of charge due to its ability to discriminate the different chemical environments or electronic configurations manifested by chemical shifts of core level lines in high-resolution spectra. Since the photoemission process is inherently fast (well below the femtosecond time scale), dynamic processes can be efficiently explored. We determine here the fingerprint of partial oxidation on the photoemission lines of nanoparticles of selected TTF-based conductors.

CONTRADICTION TO THE TABLE OF D. I. MENDELEEV AND THEIR ELIMINATION

The article discusses a new approach to the formation of periods of the Periodic Table of Mendeleev. With the help of the new formula and the first proposed quantum states of the outer electron shells of atoms of chemical elements, the periods of the periodic table are reformatted. It is supposed to reduce the number of periods in the table by introducing the corresponding sub-periods. This is confirmed by the material given in the article. The following description of the order of formation of electron layers is proposed: the principal quantum number (n), then the newly proposed quantum states of electrons («first» and «second»), which in turn constitute the electronic configurations of sub-periods in periods, and only then the remaining quantum orbitals (s, p, d and f).

Structural tuning of heterogeneous molecular catalysts for electrochemical energy conversion

Heterogeneous molecular catalysts based on transition metal complexes have received increasing attention for their potential application in electrochemical energy conversion. The structural tuning of first and second coordination spheres of complexes provides versatile strategies for optimizing the activities of heterogeneous molecular catalysts and appropriate model systems for investigating the mechanism of structural variations on the activity. In this review, we first discuss the variation of first spheres by tuning ligated atoms; afterward, the structural tuning of second spheres by appending adjacent metal centers, pendant groups, electron withdrawing/donating, and conjugating moieties on the ligands is elaborated. Overall, these structural tuning resulted in different impacts on the geometric and electronic configurations of complexes, and the improved activity is achieved through tuning the stability of chemisorbed reactants and the redox behaviors of immobilized complexes.

Super Transition Arrays: A Tool for Studying Spectral Properties of Hot Plasmas

For the theoretical study of X and extreme-UV spectra of ions in plasmas, quantum mechanics brings more detailed results than statistical physics. However, it is impossible to handle individually the billions of levels that must be taken into account in order to properly describe hot plasmas. Such levels can be gathered into electronic configurations or superconfigurations (groups of configurations) and the corresponding calculations rely on appropriate statistical methods, for local or non-local thermodynamic equilibrium plasmas. In this article we present the basic principles of the Super-Transition-Array approach as well as its practical implementation. During the last decades, calculations performed with the SCO code (Superconfiguration Code for Opacity) have been compared to opacity measurements. The code includes static screening of ions by plasma and is well suited for studying plasma density effects (for example pressure ionization) on opacity and equation of state. The recently developed SCO-RCG code (Superconfiguration Code for Opacity combined with Robert Cowan’s “G” subroutine) combines statistical methods from SCO and fine-structure (detailed-level-accounting) calculations using subroutine RCG from Cowan’s code. SCO-RCG enables us to obtain very detailed spectra and to significantly improve the interpretation of experimental spectra. The Super-Transition-Array formalism is still the cornerstone of several opacity codes, and new ideas are emerging, such as the Configurationally Resolved-Super-Transition-Array approach or the extension of the Partially Resolved-Transition-Array concept to the superconfiguration method.

1.3 Modelling Radicals and Their Reactivities

In this chapter, the application of computational quantum mechanical methods to the understanding of radical reactions is introduced. For radical reactions, access to electronic configurations through quantum chemical calculations allows rationalization of unusual reactivities. Using the valence bond approach, the nature of bonding in three-electron bonds can be characterized by large resonance interactions. Similarly, some simple reactions that are commonly believed to be radical-free, such as [3 + 2] cycloadditions, are in fact governed by a high-lying biradical intermediate that helps to stabilize the transition state. More complex radical and enzymatic reactions can also be modelled, as illustrated by the example of horseradish peroxidase. These case studies show that computational analysis can complement experimental investigations and fill in the blanks to enable a more complete understanding of radical reactions.