Applications of a graph related to conjugacy classes in finite groups

This article was written by the authors with a during the forth author's visit to Milano and, independently.     

Synthesis and biological evaluation of analogues of butyrolactone I and molecular model of its interaction with CDK2

A series of analogues of butyrolactone I, a natural product isolated from Aspergillus terreus that selectively inhibits the CDK2 and CDK1 kinases and that has been found to exhibit an interesting antiproliferative activity, have been synthesized. Its antitumor activity has been tested. Molecular models of the complex between butyrolactone I and the CDK2 active site have been built using a combination of conformational search and automated docking techniques. The stability of the resulting complexes has been assessed by molecular dynamics simulations and the experimental results obtained for the synthesized analogues are rationalized based on the molecular models.     

Reactions of potent antitumor complex trans-[Ru(III)Cl4(indazole)2]- with a DNA-relevant nucleobase and thioethers: insight into biological action

Reactions of the complex trans-[RuCl(4)(Hind)(2)](-) (Hind = indazole), which is of clinical relevance today, with both the DNA model nucleobase 9-methyladenine (made) and the thioethers R(2)S (R = Me, Et), as models of the methionine residue in biological molecules possibly acting as nitrogen-competing sulfur-donor ligands for ruthenium atom, have been investigated to get insight into details of mechanism leading to antitumor activity. Three novel ruthenium complexes, viz., [Ru(III)Cl(3)(Hind)(2)(made)], 1, [Ru(II)Cl(2)(Hind)(2)(Me(2)S)(2)], 2, and [Ru(II)Cl(2)(Hind)(2)(Et(2)S)(2)], 3, have been isolated as solids. Oxidation of 2 and 3 with hydrogen peroxide in the presence of 12 M HCl in chloroform afforded the monothioether adducts, viz., [Ru(III)Cl(3)(Hind)(2)(Me(2)S)], 4, and [Ru(III)Cl(3)(Hind)(2)(Et(2)S)], 5. By dissolution of 2 or 3 in DMSO, replacement of both R(2)S ligands by DMSO molecules occurred with isolation of trans,trans,trans-[Ru(II)Cl(2)(Hind)(2)(DMSO)(2)], 6. The products were characterized by elemental analysis, IR, UV-vis, electrospray mass spectrometry, cyclic voltammetry, and X-ray crystallography (1.CH(2)Cl(2).CH(3)OH and 1.1.1H(2)O.0.9CH(3)OH, 2, and 5). The first crystallographic evidence for the monofunctional coordination of the 9-methyladenine ligand to ruthenium via N7 and the self-pairing of the complex molecules via H-bonding, using the usual Watson-Crick pairing donor and acceptor sites of two adjacent 9-methyladenine ligands, is reported. The electrochemical behavior of 1-5 has been studied in DMF and DMSO by cyclic voltammetry. The redox potential values have been interpreted on the basis of the Lever's parametrization method. The E(L) parameter was estimated for 9-methyladenine at 0.18 V, showing that this ligand behaves as a weaker net electron donor than imidazole (E(L) = 0.12 V). The kinetics of the reductively induced stepwise replacement of chlorides by DMF in 4 and 5 were studied by digital simulation of the cyclic voltammograms. The rate constant k(1) has been determined as 0.9 +/- 0.1 s(-)(1), which obeys the first-order rate law, while k(2) is concentration dependent (0.2 +/- 0.1 M(1)(-)(n)().s(-)(1) with n > 1 for 4 mM solutions of 4 and 5), indicating higher-order reactions mechanism.     

Mixed‐Ligand Complexes of Zinc(II) with α‐Hydroxycarboxylates and Aromatic N‐N Donor Ligands: Synthesis,Crystal Structures and Effect of Weak Interactions on their Crystal Packing

Several new two‐ligand complexes of zinc(II) with the aromatic N, N‐donor ligands 2, 2′‐bipyridine or 1, 10‐phenanthroline and one of three different α‐hydroxycarboxylates (HL′) derived of the α‐hydroxycarboxylic acids (H₂L′) (2‐methyllactic, H₂mL; mandelic, H₂M or benzilic, H₂B) were prepared. The compounds of formula [Zn(HL′)₂(NN)]·nH₂O (HL′ = HM, HB) were isolated as white powders and characterized by elemental analysis, IR spectroscopy and thermogravimetric analysis. The complexes of general formula [Zn(HL′)(NN)₂](HL′)·nH₂O (HL′ = HmL, HM) and [Zn(HB)₂(NN)₂], were obtained as single crystals and were characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis and X‐ray diffractometry. In all cases, the zinc atom is in a distorted octahedral environment. In [Zn(HL′)(NN)₂](HL′)·nH₂O the α‐hydroxycarboxylato ligands behave as bidentate chelating monoanion and an α‐hydroxycarboxylate as counterion is also present. In [Zn(HB)₂(NN)₂], the monoanionic benzilato ligand behaves as monodentate through one oxygen atom of the carboxylate function. The effect of the classical and no‐classical hydrogen bonding and of the π‐π and C‐H…π interactions in the 3D supramolecular arrangement of these molecular complexes is analyzed.     

The fluorobenzene-argon S(1) excited-state intermolecular potential energy surface

We evaluate the first excited-state (S1) intermolecular potential energy surface for the fluorobenzene-Ar van der Waals complex using the coupled cluster method and the augmented correlation-consistent polarized valence double-zeta basis set extended with a set of 3s3p2d1f1g midbond functions. To calculate the S(1) interaction energies, we use ground-state interaction energies evaluated with the same basis set and the coupled cluster singles and doubles (CCSD) including connected triple excitations [CCSD(T)] model and interaction and excitation energies evaluated at the CCSD level. The surface minima are characterized by the Ar atom located above and below the fluorobenzene ring at a distance of 3.5060 A with respect to the fluorobenzene center of mass and at an angle of 5.89 degrees with respect to the axis perpendicular to the fluorobenzene plane. The corresponding interaction energy is -425.226 cm(-1). The surface is used in the evaluation of the intermolecular level structure of the complex, and the results are compared to the experimental data available and to those found in previous theoretical papers on ground-state potentials for similar complexes.     

Rare earth arenedisulfonate metal-organic frameworks: an approach toward polyhedral diversity and variety of functional compounds

Eight 2D and 3D metal-organic framework (MOF) rare earth naphthalenedisulfonates have been obtained. The different geometry of the naphthalenedisulfonic acids used as connectors [(1,5-NDS) and (2,6-NDS)] gives rise to the three new structure types. In Ln(OH)(1,5-NDS)H2O, LnPF-1 (lanthanide polymeric framework; Ln=La, Nd, Pr, Sm and Eu), the lanthanide ion is octacoordinated. Its 3D structure is formed by (Ln2O14)-S-(Ln2O14) infinite chains, connected through complete NDS connectors. LnPF-2 (Ln=Nd), with the same empirical formula as the former, and the lanthanide in octa- and nonacoordination, owns an arrangement of sulfonate bridges and neodymium polyhedra that gives rise to a 2D structure. [Ln5(2,6-NDS)3(OH)9(H2O)4](H2O)2, LnPF-3 (Ln=Nd, Eu), demonstrates that it is possible to obtain a 3D structure with (2,6-NDS), when a greater Ln/connector ratio is employed. It is worth pointing out the existence, in this latter family of compounds, of a mu5-OH group, whose hydrogen atom is very close to one-sixth Ln atom (distance Ln...H=2.09 A). The materials, with high thermal stability, act as active and selective bifunctional heterogeneous catalysts in oxidation of linalool yielding cyclic hydroxy ethers. The absence of any 3D Nd-Nd magnetic interaction is explained due to the inner nature of 4f orbitals of Nd3+, which do not favor the magnetic exchange. The influence of the polymeric frame matrix results in a better photoluminescence efficiency for NdPF-1.     

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19. We present here structural models and dynamics of the helicase in complex with its native substrates based on thorough analysis of homologous sequences and existing experimental structures. We performed and analysed microseconds of molecular dynamics (MD) simulations, and our model provides valuable insights to the binding of the ATP and ssRNA at the atomic level. We identify the principal motions characterising the enzyme and highlight the effect of the natural substrates on this dynamics. Furthermore, allosteric binding sites are suggested by our pocket analysis. Our obtained structural and dynamical insights are important for subsequent studies of the catalytic function and for the development of specific inhibitors at our characterised binding pockets for this promising COVID-19 drug target.

The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19.