Complexes of Zn(II)–Triazoles with CO2 and H2O: Structures, Energetics, and Applications

Using a first-principle methodology, we investigate the stable structures of the nonreactive and reactive clusters formed between Zn2+–triazoles ([Zn2+-Tz]) clusters and CO2 and/or H2O. In sum, we characterized two modes of bonding of [Zn2+-Tz] with CO2/H2O: the interaction is established through (i) a covalent bond between Zn2+ of [Zn2+-Tz] and oxygen atoms of CO2 or H2O and (ii) hydrogen bonds through N–H or C–H of [Zn2+-Tz] and oxygen atoms of H2O or CO2, N–H···O. We also identified intramolecular proton transfer processes induced by complexation. Indeed, water drastically changes the shape of the energy profiles of the tautomeric phenomena through strong lowering of the potential barriers to tautomerism. The comparison to [Zn2+-Im] subunits formed with Zn2+ and imidazole shows that the efficiency of Tz-based compounds for CO2 capture and uptake is due to the incorporation of more accessible nitrogen donor sites in Tzs compared to imidazoles. Since [Zn2+-Tz] clusters are subunits of an organometallic nanoporous materials and Zn–proteins, our data are useful for deriving force fields for macromolecular simulations of these materials. Our work also suggests the consideration of traces of water to better model the CO2 sequestration and reactivity on macromolecular entities such as pores or active sites.This is the peer-reviewed version of the article: J. Phys. Chem. A 2019, 123, 26, 5555-5565, [https://doi.org/10.1021/acs.jpca.9b03228]Published version: [http://cer.ihtm.bg.ac.rs/handle/123456789/3270

Supporting material for: "In silico design of a new Zn-triazole based metal-organic framework for CO2 and H2O adsorption"

Figure S1: Convergence of the total energy with plane wave cut-off and k point sampling mesh for MAF-66. Figure S2: Pore size distributions of MAF-66 (left) and ZTF (right). Figure S3: DFT optimized structures of parts of the supercells of ZTF (left) and MAF-66 (right) with one CO2 molecule inside. Figure S4: DFT optimized structure of parts of the supercell of MOF-66 with of one water molecule inside.Supplementary material for: J. Chem. Phys. 154, 024303 (2021); doi: [https://dx.doi.org/10.1063/5.0037594]Published version of the article: [https://cer.ihtm.bg.ac.rs/handle/123456789/4511

Half-sandwich ruthenium(II)-arene complexes: synthesis, spectroscopic studies, biological properties, and molecular modeling

In search for antitumor metal-based drugs that would mitigate the severe side-effects of cisplatin, Ru(II) complexes are gaining increasing recent interest. In this work, we report on the synthesis, characterization (1H- and 13C-NMR, FT-IR), and cytotoxicity studies of two new half-sandwich organometallic Ru(II) complexes of the general formula [Ru(η6-arene)(XY)Cl](PF6) where arene = benzene or toluene and XY = bidentates: dipyrido[3,2-a:2′,3′-c]phenazine (dppz) or 2-(9-anthryl)-1H-imidazo[4,5-f][1,10]phenanthroline (aip), which are bound to Ru(II) via two phenanthroline-N atoms in a characteristic “piano-stool” configuration of Ru(II)-arene complexes—as confirmed by vibrational and NMR spectra. In addition, cytotoxic studies were performed for similar half-sandwich organometallic [Ru(η6-p-cymene)(Me2dppz)Cl]PF6 complex (Me2dppz = 11,12-dimethyl-dipyrido[3,2-a:2′,3′-c]phenazine). This study is complemented with elaborate modeling with density functional theory (DFT) calculations, which provided insight into reactive sites of Ru(II) structures, further detailed by molecular docking on the B-DNA dodecamer, which identified binding sites and affinities: most pronounced for the [Ru(η6-benzene)(aip)Cl](PF6) in both A-T and G-C regions of the DNA minor groove. Cytotoxic activity was probed versus tumor cell lines B16, C6, and U251 (B16 mouse melanoma, C6 rat glioma, U251 human glioblastoma) and non-tumor cell line HACAT (HACAT normal human keratinocytes).This is the peer-reviewed version of the following article:Nikolić, S.; Grgurić-Šipka, S.; Djordjević, I. S.; Dahmani, R.; Dekanski, D.; Vidičević, S.; Tošić, J.; Mitić, D.; Grubišić, S. Half-Sandwich Ruthenium(II)-Arene Complexes: Synthesis, Spectroscopic Studies, Biological Properties, and Molecular Modeling. Journal of Coordination Chemistry 2019, 72 (1), 148–163. [https://doi.org/10.1080/00958972.2018.1553298].Supplementary material: [http://cherry.chem.bg.ac.rs/handle/123456789/3753

The furan microsolvation blind challenge for quantum chemical methods: First steps

© 2018 Author(s). Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH-O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication

The first microsolvation step for furans : new experiments and benchmarking strategies

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight

Early Steps in the O₂ Scavenger Process in the Aqueous Phase: Hydrazine vs DEHA

International audienceWe investigate the first direct proton abstraction reactions from reducing agents (RAHs) hydrazine and diethyl hydroxylamine (DEHA), toward dioxygen (O2) in the aqueous phase, spanning ambient to high-temperature conditions. Quantum chemistry methods and molecular dynamics simulations are employed in this study. Quantum chemistry methods are used to analyze the quasi-equilibrium between a reactive conformation and a transition state in the [RAH,O2] cluster. On the other hand, molecular dynamics simulations estimate the probability of observing a reactive conformation of the [RAH,O2] cluster in the solution. In this study, we assume that the energy barrier of the quasi-equilibrium is sufficiently high for the [RAH,O2] association process to be at equilibrium. Our findings indicate that the first proton abstraction process from a reactive conformation cluster by DEHA is energetically favored compared to hydrazine. Conversely, the association process of hydrazine and O2 in solution is more favorable than that of DEHA. Consequently, the rate constant for the first proton abstraction process is similar for both hydrazine and DEHA, particularly at high temperatures, with activation energies of approximately 21.5 ± 1.5 kcal mol–1 for both compounds. These results align with recent experiments investigating the complete O2 scavenger process in liquid water with hydrazine and DEHA. Therefore, our findings support the assumption that first proton abstraction reactions are the rate-determining steps in O2 scavenger processes in the aqueous phase

An antibacterial lead identification of novel 1,3,4-oxadiazole derivatives based on molecular computer aided design approaches

Merging Density Functional Theory (DFT) with the Quantitative Structure-Activity Relationship (2D/3D-QSAR) modeling represents a promising avenue for exploring antibacterial activity and discovering potential drugs effective against both gram-positive and gram-negative microorganisms. In this study, we employed this integrated approach to investigate a newly synthesized and promising class of 1,3,4-oxadiazole derivatives renowned for their high performance as antibacterial agents. To ensure an accurate characterization and thorough description of the targeted biological activity, we systematically evaluated various DFT functionals to precisely predict the geometrical and electronic descriptors of the investigated compounds. These descriptors were crucial for developing and validating the proposed 2D/3D-QSAR models. Our results reveal that the introduction of a donor group enhances the antibacterial activity of the derivatives. The analysis of molecular descriptors underscores the positive impact of this modification on the compounds' efficacy against bacteria. Additionally, our experimental compounds exhibit favorable characteristics concerning oral bioavailability, a crucial aspect in drug development. The identification of robust correlations between antibacterial activity and specific descriptors was achieved by conducting an extensive analysis that encompassed multiple linear regression (MLR), Random Forest (RF), and Artificial Neural Networks (ANN). Subsequently, a partial least squares (PLS) model was employed to construct 3D-QSAR models based on the Comparative Molecular Field Analysis (CoMFA) and Comparative Similarity Indices Analysis (CoMSIA) descriptors. Validation of the output models was performed using leave-one-out and bootstrapping strategies. The resultant 2D/3D-QSAR models demonstrated a high correlation between experimental and predicted activity values. Leveraging these models, the developed MLR model, expressed as pMIC = -12.704 + 0.260 logP – 6.104 10-03 SAG – 51.385 qN33, serves as a valuable tool for predicting antibacterial activity. we indicate that the machine learning methods, Artificial Neural Networks (ANN) and Random Forest (RF), outperform traditional models in accurately predicting antibacterial activity. We designed ten novel molecules, subjecting them to molecular docking and molecular dynamics simulations to predict their optimal postures when docked in the target and gain insights into the formed interactions. Additionally, Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis was applied to discern the potential behavior of these novel compounds in the human body. As a result, the newly suggested chemical, X4, X10, exhibited robust inhibitory potential against gram-negative microbes

In Sicilia sbarcati 800 migranti, altri seicento in arrivo. Ad Augusta i 24 morti dell'ultimo naufragio, repubblica.it, 27/08/2014

"I dispersi al largo della Libia sarebbero un centinaio. Tra i profughi approdati a Pozzallo c'era anche un gatto. Salvata una bimba di 14 mesi aggrappata a una tavola C'erano anche 81 donne e 133 minori tra i 449 migranti siriani, palestinesi ed egiziani arrivati a Pozzallo, nel ragusano, le cui operazioni di sbarco sono terminate intorno alle due della scorsa notte. Con il gruppo degli immigrati c'era anche un gatto, sottoposto poi a visita veterinaria per verificare che non fosse portatore..