Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Effects of Ionic Liquids on the Thermodynamics of Hydrogen Activation by Frustrated Lewis Pairs: A Density Functional Theory Study**

Nowadays, hydrogen activation by frustrated Lewis pairs (FLPs) and their applications are one of the emerging research topics in the field of catalysis. Previous studies have shown that the thermodynamics of this reaction is determined by electronic structures of FLPs and solvents. Herein, we investigated systems consisting of typical FLPs and ionic liquids (ILs), which are well known by their large number of types and excellent solvent effects. The density functional theory (DFT) calculations were performed to study the thermodynamics for H₂ activation by both inter- and intra-molecular FLPs, as well as the individual components. The results show that the computed overall Gibbs free energies in ILs are more negative than that computed in toluene. Through the thermodynamics partitioning, we find that ILs favor the H−H cleavage elemental step over the elemental steps of proton attachment, hydride attachment and zwitterionic stabilization. Moreover, the results show that these effects are strongly dependent on the type of FLPs, where intra-molecular FLPs are more affected compared to the inter-molecular FLPs.     

Influence of ionic liquid counterions on activity and selectivity of ethylene trimerization using chromium-based catalysts in biphasic media

In recent years ionic liquids (ILs) have attracted much interest because of their widespread use in various fields. Several trimerization and oligomerization catalysts have been evaluated in ILs with different organic–inorganic hybrid structures. High catalytic activity and selectivity, easy product separation, and recycling of the catalyst are the advantages of a biphasic catalyst system compared to the homogeneous catalysts. In this study, the influence of IL counter-anions on activity and selectivity of the ethylene trimerization catalysts based on Cr-SNS-R was investigated. All synthesized materials were characterized using Fourier-transform infrared spectroscopy, ¹H NMR, ¹³C NMR, UV–Vis. spectroscopy, thin-layer chromatography, and elemental analysis (CHNS). In ethylene trimerization reaction, the dodecyl substituent in the SNS ligand exhibited better activity and selectivity than the butyl substituent. The results revealed that the presence of BF₄⁻ as a counter-anion in the IL led to an increase in activity and selectivity compared to Br⁻ and I⁻ counter-anions. It was found that the BF₄⁻ counter-anion plays a conclusive role in the development of 1-hexene activity and selectivity to a maximum amount of 71,132 g_1-C6/(g_Cr × h) and more than 99%, respectively. Finally, the catalyst was reused thrice without losing its 1-hexene selectivity.     

Analyses of reaction rate data for the simple hydrolysis of acetic anhydride in the acetonitrile/water and acetone/water cosolvent systems using recently developed thermodynamic rate equations

This article presents reaction rate data for the simple hydrolysis of acetic anhydride in the acetonitrile/water and acetone/water cosolvent systems and regression analyses using recently developed thermodynamic rate equations that contain electrostatic and solvent-solute terms. The isomole fraction plots for these reaction systems are linear, and previous theoretical work has shown that the electrostatic term is negligible for such systems. On the other hand, the reaction rates are dependent upon the cosolvent mole fraction, indicating that the solvent-solute term, which is modeled empirically, is significant. The results of the analyses provide the foundation for a paradigm shift away from the emphasis on electrostatic effects to more tenable explanations of kinetic behavior in solvent systems.     

In Situ Structural Determination of a Homogeneous Ruthenium Racemization Catalyst and Its Activated Intermediates Using X-Ray Absorption Spectroscopy

The activation process of a known Ru-catalyst, dicarbonyl(pentaphenylcyclopentadienyl)ruthenium chloride, has been studied in detail using time resolved in situ X-ray absorption spectroscopy. The data provide bond lengths of the species involved in the process as well as information about bond formation and bond breaking. On addition of potassium tert-butoxide, the catalyst is activated and an alkoxide complex is formed. The catalyst activation proceeds via a key acyl intermediate, which gives rise to a complete structural change in the coordination environment around the Ru atom. The rate of activation for the different catalysts was found to be highly dependent on the electronic properties of the cyclopentadienyl ligand. During catalytic racemization of 1-phenylethanol a fast-dynamic equilibrium was observed.     

EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods

Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.     

Female Faculty: Why So Few and Why Care?

Despite slow ongoing progress in increasing the representation of women in academia, women remain significantly under-represented at senior levels, in particular in the natural sciences and engineering. Not infrequently, this is downplayed by bringing forth arguments such as inherent biological differences between genders, that current policies are adequate to address the issue, or by deflecting this as being “not my problem” among other examples. In this piece we present scientific evidence that counters these claims, as well as a best-practice example, Genie, from Chalmers University of Technology, where one of the authors is currently employed. We also highlight particular challenges caused by the current COVID-19 pandemic. Finally, we conclude by proposing some possible solutions to the situation and emphasize that we need to all do our part, to ensure that the next generation of academics experience a more diverse, inclusive, and equitable working environment.     

Dicationic disiloxane ionic liquids

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Hydrolytic polycondensation of trimethoxymethylsilane under ultrasonic irradiation

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Direct UVC photodegradation of imipramine in aqueous solutions: a mechanistic study

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