Bovine serum albumin uptake and polypeptide disaggregation studies of hypoglycemic ruthenium(II) uracil Schiff-base complexes

Our prior studies have illustrated that the uracil ruthenium(II) diimino complex, [Ru(H3ucp)Cl(PPh3)] (1) (H4ucp = 2,6-bis-((6-amino-1,3-dimethyluracilimino)methylene)pyridine) displayed high hypoglycemic effects in diet-induced diabetic rats. To rationalize the anti-diabetic effects of 1, three new derivatives have been prepared, cis-[Ru(bpy)2(urdp)]Cl2 (2) (urdp = 2,6-bis-((uracilimino)methylene)pyridine), trans-[RuCl2(PPh3)(urdp)] (3), and cis-[Ru(bpy)2(H4ucp)](PF6)2 (4). Various physicochemical techniques were utilized to characterize the structures of the novel ruthenium compounds. Prior to biomolecular interactions or in vitro studies, the stabilities of 1-4 were monitored in anhydrous DMSO, aqueous phosphate buffer containing 2% DMSO, and dichloromethane (DCM) via UV-Vis spectrophotometry. Time-dependent stability studies showed ligand exchange between DMSO nucleophiles and chloride co-ligands of 1 and 3, which was suppressed in the presence of an excess amount of chloride ions. In addition, the metal complexes 1 and 3 are stable in both DCM and an aqueous phosphate buffer containing 2% DMSO. In the case of compounds 2 and 4 with no chloride co-ligands within their coordination spheres, high stability in aqueous phosphate buffer containing 2% DMSO was observed. Fluorescence emission titrations of the individual ruthenium compounds with bovine serum albumin (BSA) showed that the metal compounds interact non-discriminately within the protein's hydrophobic cavities as moderate to strong binders. The metal complexes were capable of disintegrating mature amylin amyloid fibrils. In vivo glucose metabolism studies in liver (Chang) cell lines confirmed enhanced glucose metabolism as evidenced by the increased glucose utilization and glycogen synthesis in liver cell lines in the presence of complexes 2-4.

Isolation, crystal structure and DFT study of 2,2,6,6-tetramethyl-4-oxo-piperidinium nitrate isolated from the stembark of Vitex doniana (Lamiaceae)

We present the results of the analysis of 2,2,6,6-tetramethyl-4-oxo-piperidinium nitrate isolated from the stem bark of Vitex doniana, a tree growing in Nigeria. The low-temperature molecular structure comprises one 2,2,6,6-tetramethyl-4-oxopiperidinium cation and one nitrate anion as one molecule in the asymmetric unit. The compound crystallizes in the monoclinic space group P21/n. A portion of the nitrate anion exhibits positional disorder with the main disorder component present 66.253(2) % of the time and the minor disorder component present 33.279(2) % of the time. In comparison with the previously reported room-temperature structure of C9H18N2O4 . The low-temperature structure shows similarity with the piperidinium ring adopting a slightly deformed chair conformation while the nitrate anion is disordered. DFT method was used to complement the experimental study.

Synthesis, Structure, Hirshfeld Surface Analysis, Non-Covalent Interaction, and In Silico Studies of 4-Hydroxy-1-[(4-Nitrophenyl)Sulfonyl]Pyrrolidine-2-Carboxyllic Acid

The new compound 4-hydroxy-1-[(4-nitrophenyl)sulfonyl]pyrrolidine-2-carboxyllic acid was obtained by the reaction of 4-hydroxyproline with 4-nitrobenzenesulfonyl chloride. The compound was characterized using single crystal X-ray diffraction studies. Spectroscopic methods including NMR, FTIR, ES-MS, and UV were employed for further structural analysis of the synthesized compound. The title compound was found to have crystallized in an orthorhombic crystal system with space group P212121. The S1-N1 bond length of 1.628 (2) Å was a strong indication of the formation of the title compound. The absence of characteristic downfield 1H NMR peak of pyrrolidine ring and the presence of S-N stretching vibration at 857.82 cm-1 on the FTIR are strong indications for the formation of the sulfonamide. The experimental study was complemented with computations at the B3LYP/6-311G +  + (d,p) level of theory to gain more understanding of interactions in the compound at the molecular level. Noncovalent interaction, Hirsfeld surface analysis and interaction energy calculations were employed in the analysis of the supramolecular architecture of the compound. Predicted ADMET parameters, awarded suitable bioavailability credentials, while the molecular docking study indicated that the compound enchants promising inhibition prospects against dihydropteroate synthase, DNA topoisomerase, and SARS-CoV-2 spike.

Graphical Abstract

Herein we present the solid state structure, noncovalent interaction and spectroscopic analysis of a prospective bioactive compound 4-hydroxy-1-[(4-nitrophenyl)sulphonyl]pyrrolidine-2-carboxyllic acid.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10870-023-00978-0.

A study of the thermodynamics and mechanisms of the atmospherically relevant reaction dimethyl sulphide (DMS) with atomic chlorine (Cl) in the absence and presence of water, using electronic structure methods

The thermodynamics and mechanisms of the atmospherically relevant reaction dimethyl sulphide (DMS) + atomic chlorine (Cl) were investigated in the absence and presence of a single water molecule, using electronic structure methods. Stationary points on each reaction surface were located using density functional theory (DFT) with the M06-2X functional with aug-cc-pVDZ (aVDZ) and aug-cc-pVTZ (aVTZ) basis sets. Then fixed point calculations were carried out using the UM06-2X/aVTZ optimised stationary point geometries, with aug-cc-pVnZ basis sets (n = T and Q), using the coupled cluster method [CCSD(T)], as well as the domain-based local pair natural orbitals coupled cluster [DLPNO-UCCSD(T)] approach. Four reaction channels are possible, formation of (A) CH₃SCH₂ + HCl, (B) CH₃S + CH₃Cl, (C) CH₃SCl + CH₃, and (C') CH₃S(Cl)CH₃. The results show that, in the absence of water, channels A and C' are the dominant channels. In the presence of water, the calculations show that the reaction mechanisms for A and C formation change significantly. Channel A occurs via submerged TSs and is expected to be rapid. Channel B occurs via TSs which present significant energy barriers indicating that this channel is not significant in the presence of water relative to CH₃SCH₂ + HCl and DMS·Cl adduct formation, as is the case in the absence of water. Channel C was not considered as it is endothermic in the absence of water. In the presence of water, pathways which proceed via (a) DMS·H₂O + Cl, (b) Cl·H₂O + DMS and (c) DMS·Cl + H₂O were considered. It was found that under tropospheric conditions, reactions via pathway (b) are of minor importance relative to those that proceed via pathways (a) and (c). This study has shown that water changes the mechanisms of the DMS + Cl reactions significantly but the presence of water is not expected to affect the overall reaction rate coefficient under atmospheric conditions as the DMS + Cl reaction has a rate coefficient at room temperature close to the collisional limit.

Computational study of the interaction of the psychoactive amphetamine with 1,2-indanedione and 1,8-diazafluoren-9-one as fingerprinting reagents

In this study, we used computational methods to investigate the interaction of amphetamine (AMP) with 1,2-indanedione (IND) and 1,8-diazafluoren-9-one (DFO) so as to understand whether AMP can be detected in latent fingerprints using either of these reagents. The results show that the binding energies of AMP with IND and DFO were enhanced by the presence of amino acid from -9.29 to -12.35 kcal mol^-1 and -7.98 to -10.65 kcal mol^-1, respectively. The physical origins of these interactions could be better understood by symmetry-adapted perturbation theory. The excited state properties of the binding structures with IND demonstrate distinguishable absorption peaks in the UV-vis spectra but zero fluorescence. Furthermore, the UV-vis spectra of the possible reaction products between AMP and the reagents reveal absorption peaks in the visible spectrum. Therefore, we could predict that reaction of AMP with IND would be observable by a reddish colour while with DFO, a colour change to violet is expected. To conclude, the reagents IND and DFO may be used to detect AMP by UV-vis spectroscopy and if their reactions are allowed, the reagents may then act as a potentially rapid, affordable and easy colorimetric test for AMP in latent fingerprints without destruction of the fingerprint sample.

Physicochemical analysis of wastewater generated from a coating industry in Mauritius

The coating industry is one of the most important consumers of water and chemicals and consequently is a major water polluter in Mauritius. The focus of this study was to characterise wastewater generated by a coating industry in Mauritius. The objectives were to develop a wastewater sampling strategy and to analyse the pollutant parameters as per Mauritian regulations. The wastewater samples were analysed for physicochemical properties and metal abundances over a period of 6 months. The physicochemical parameters analysed were pH, electrical conductivity (EC), true colour, total suspended solids (TSS), biological oxygen demand (BOD₅), chemical oxygen demand (COD), nitrate, phosphate, sulphate and free chlorine. The wastewater samples were also analysed for metal ions such as sodium, potassium, arsenic, cadmium, chromium, cobalt, copper, iron, lead, manganese, mercury, molybdenum, nickel and zinc. The results of the physicochemical parameters indicated the presence of biologically resistant organic matters in all the wastewater samples with elevated values of BOD₅ and COD, and low biodegradability index, respectively. The coating industry wastewater samples were acidic and saline in nature. Moreover, they presented high concentrations of TSS, free chlorine and sodium ions compared to standard limits promulgated by the Mauritian Government. Spearman's rank correlation matrix with non-linear regression analysis showed significant associations among the measured parameters which were found to have a common origin in the coating industry wastewater. This research will be useful for regular monitoring and setting up an adequate coating industry wastewater treatment for the potential reuse in production processes in Mauritius.

Experimental and theoretical study of the dye-sensitized solar cells using Hibiscus sabdariffa plant pigment coupled with polyaniline/graphite counter electrode

In this research work, the extraction, characterization, device fabrication, and theoretical investigation of Hibiscus sabdariffa plant extract, for possible application in solid DSSCs, are reported. The plant extract was analyzed using FT-IR and UV–Vis spectrophotometry. Polyaniline on graphene was used as the counter electrode whereas titanium (IV) oxide was used as the photo anode for the fabricated DSSCs. The experimental results obtained for the open circuit voltage, short circuit current density, field factor, maximum power and conversion efficiency are 0.925 V, 0.073 A/cm2, 1.43, 1.04 W, and 0.044 % respectively. The excited states of anthocyanin (delphinidin) and quercetin, the most stable structures of Hibiscus sabdariffa plant extract, were studied using density functional theory method. In addition, the theoretical open circuit voltage, light harvesting efficiency, coupling constant, free energy change, and HOMO–LUMO energy gap were predicted for the photovoltaic properties. The theoretical results suggest that quercetin has relatively better photovoltaic properties and, hence, potentially a better dye for solar cell application.

Synthesis, characterization, DFT and molecular docking studies of acetone O-((2,5-dichlorophenyl)sulfonyl) oxime

Acetone O-((2,5-dichlorophenyl)sulfonyl) oxime was prepared from 2,5-dichlorophenylsulfonyl chloride and acetone oxime using triethylamine. The compound was characterized using 1H NMR and 13C NMR spectra. Molecular docking was performed with the compound and cholinesterase enzymes. The average affinity of the compound with the acetylcholinesterase and butyrylcholinesterase was calculated at −7.46 ± 0.14 and −6.70 ± 0.00 kcal/mol, respectively. The density functional theory method was also used to complement the experimental study. The findings of this work might be useful towards the applications of the compound studied.

Decoding the reaction mechanism of the cyclocondensation of ethyl acetate2-oxo-2-(4-oxo-4H-pyrido [1.2-a] pyrimidin-3-yl) polyazaheterocycle and ethylenediamine using bond evolution theory

We investigated the flow of electron density along the cyclocondensation reaction between ethyl acetate 2-oxo-2-(4-oxo-4H-pyrido[1.2-a]pyrimidin-3-yl) polyazaheterocycle (1) and ethylenediamine (2) at the ωB97XD/6-311++G(d,p)computational method within of bond evolution theory (BET). The exploration of potential energy surface shows that this reaction has three channels (1-3) with the formation of product 3 via channel-2 (the most favorable one) as the main product and this is in good agreement with experimental observations. The BET analysis allows identifying unambiguously the main chemical events happening along channel-2. The mechanism along first step (TS2-a) is described by a series of four structural stability domains (SSDs), while five SSDs for the last two steps (TS2-b and TS2-c). The first and third steps can be summarized as follows, the formation of N1-C6 bond (SSD-II), then, the restoration of the nitrogen N1 lone pair (SSD-III), and finally, the formation of the last O1-H1 bond (SSD-IV). For the second step, the formation of hydroxide ion is noted, as a result of the disappearance of V(C6,O7) basin and the transformation of C6-N1 single bond into double one (SSD-IV). Finally, the appearance of V(O7,H2) basin lead to the elimination of water molecule within the last domain is observed.

ExcelAutomat 1.4: generation of supporting information

Quantum chemical computations generate output files with data. The processing of these data generates results which are presented in a target document, such as a manuscript or supporting information (SI). Several tools and techniques can be employed to facilitate the transfer of data which, otherwise, can be time-consuming with a large number of files. However, depending on the user’s technical knowledge or expertise with the software, additional time has to be invested to set up the software or use the tools. In addition, to the best of the authors’ knowledge, the tools currently available do not provide an option to transfer the data from the output files directly to the target document without the use of custom scripts. The ExcelAutomat tool (Laloo et al., J. Comput. Aided Mol. Des. 2017, 31, 667 and Laloo et al., J. Comp. Chem. 2019, 40, 3) is spreadsheet-based and was developed in-house to facilitate the steps involved in the processing of computational files. The tool was adapted to facilitate the generation of SI in an update of ExcelAutomat 1.4. A graphical user interface was designed where the options for the generation of SI can be defined. ExcelAutomat 1.4 is compatible with Microsoft Excel and the open-source LibreOffice Calc. The extensible tool supports various software packages and parameters by interfacing with the cclib library and through built-in codes. The tool provides a method to transfer data from output files directly to a Microsoft Word or LibreOffice Writer document and can reduce the number of steps, tools or technical knowledge needed to generate SI, especially for users who are familiar with Microsoft Excel or LibreOffice Calc.

Unveiling the non-polar [3+2] cycloaddition reactions of cyclic nitrones with strained alkylidene cyclopropanes within a molecular electron density theory study

The role of cyclopropane substitution on the ethylene in zw-type [3+2] cycloaddition (32CA) reactions of cyclic nitrones has been studied within Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311G(d,p) computational level. Electron Localization Function (ELF) analysis of the ethylenes shows that the presence the cyclopropane only slightly increases the electron density in the C–C bonding region. Analysis of the Conceptual DFT reactivity indices indicates that the presence of the cyclopropane does not produce any remarkable change in the reactivity of these strained ethylenes. The marginal electrophilic character of ethylene makes the zw-type 32CA reactions of non-polar character. The presence of the cyclopropane in the ethylene decreases the activation enthalpy of the 32CA reactions by only 1.7 and 2.6 kcal mol⁻¹, and also decreases the ortho regioselectivity. The loss of the strain present in the cyclopropane is responsible for the reduction of the activation enthalpy and the increase of the reaction enthalpy in these non-polar 32CA reactions. The presence of the cyclopropane does not cause any change, neither in the transition state structure (TS) geometries nor in their electronic structure. The very low global electron density transfer (GEDT) computed at the TSs confirms the non-polar character of these 32CA reactions. The ortho regioselectivity experimentally observed in these non-polar 32CA reactions is determined by the most favorable two-center interaction between the less electronegative C1 carbon of nitrone and the non-substituted methylene C5 carbon of the ethylenes.

The role of cyclopropane substitution on the ethylene in zw-type [3+2] cycloaddition (32CA) reactions of cyclic nitrones has been studied within Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311G(d,p) computational level.

Theoretical study of a derivative of chlorophosphine with aliphatic and aromatic Grignard reagents: SN2@P or the novel SN2@Cl followed by SN2@C?

The proposed SN2 reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles [Ye et al., Org. Lett., 2017, 19, 5384–5387] were studied theoretically in order to explain the observed stereochemistry of the products.

Reaction of •OH with CHCl=CH-CHF2 and its atmospheric implication for future environmental-friendly refrigerant

In order to understand the atmospheric implication of the chlorinated hydrofluoroolefin (HFO), the geometrical structures and the IR absorption cross sections of the stereoisomers 1-chloro-3,3-difluoropropene were studied using the B3LYP/6-31G(3df) and M06-2X/6-31G(3df) methods in the gas phase. The cis-trans isomerization was assessed using the M06-2X/6-311++G(3df,p)//6-31+G(3df,p) method. The latter method was also employed for thermochemistry and the rate coefficients of the reactions of •OH with the cis- and trans-isomers in the temperature ranging from 200 to 400 K. The computational method CCSD/cc-pVTZ//M06-2X/6-31+G(3df,p) was used to benchmark the rate coefficients. It turns out that, the trans-isomer is more stable than cis-isomer and the trans- to cis-isomerization is thermodynamically unfavorable. The rate coefficient follows the Gaussian law with respect to the inverse of temperature. At the global temperature of stratosphere, the calculated rate coefficients served to estimate the atmospheric lifetime along with the photochemical ozone creation potential (POCP). This yielded lifetimes of 4.31 and 7.31 days and POCPs of 3.80 and 2.23 for the cis- and trans-isomer, respectively. The radiative forcing efficiencies gave 0.0082 and 0.0152 W m−2 ppb−1 for the cis- and trans-isomer, respectively. The global warming potential approached zero for both stereoisomers at 20, 100, and 500 years time horizons.

Interaction between favipiravir and hydroxychloroquine and their combined drug assessment: in silico investigations

Hydroxychloroquine (HCQ) and favipiravir (FPV) are known to be effective antivirals, and there are reports about their use to fight the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) despite that these are not conclusive. The use of combined drugs is common in drug discovery, and thus, we investigated HCQ and FPV as a combined drug. The density functional theory method was used for the optimization of geometries, spectroscopic analysis and calculation of reactivity parameters. The quantum theory of atoms in molecules was applied to explain the nature of the hydrogen bonds and confirm the higher stability of the combined drug. We also evaluated the absorption, distribution, metabolism and excretion (ADME) parameters to assess their drug actions jointly using SwissADME. The preliminary findings of our theoretical study are promising for further investigations of more potent and selective antiviral drugs.

Synthesis, Molecular Docking and Tyrosinase Inhibitory Activity of the Decorated Methoxy Sulfonamide Chalcones: in vitro Inhibitory Effects and the Possible Binding Mode

In this study, a series of sulfonamide chalcones derivatives was synthesized and its chemical structures were confirmed by spectral characteristics. The synthesized compounds were evaluated for their tyrosinase inhibitory activities along with molecular docking study. The tyrosinase inhibitory results indicated that compounds 5b, 5c, 5f, 5g and 5h displayed the significant tyrosinase inhibitory activity and comparable to the standard drug (kojic acid). Compound 5c exhibits the most potent tyrosinase inhibition among the synthesized compounds with IC50 = 0.43±0.07 mM, L-DOPA as the substrate, and better than that of the standard kojic acid (IC50 = 0.60±0.20 mM). Molecular docking studies showed that the binding mode of some compounds is in the tyrosinase binding pocket surrounding the copper in the active site. The correlation between the docking results with IC50 values showed that the binding mode prediction of the test compounds would also be convincing. This comprehensive study allows for a possible mechanism for the antityrosinase activity of the sulfonamide chalcones. These sulfonamide chalcones bind to copper atoms of tyrosinase which responsible for the catalytic activity of tyrosinase. These compounds may be used as a lead for rational drug designing for the multi-functional tyrosinase inhibitor.

Can the Antivirals Remdesivir and Favipiravir Work Better Jointly? In Silico Insights

The proverb "Old is gold" is applicable in drug discovery and the proverb "All that Glitters is not Gold" is also appropriate. In the COVID-19 era, there has been a race for drugs to be effective against SARS-CoV-2. There are reports about the uses of Remdesivir and Favipiravir as existing antivirals against virus but none have been conclusive so far. In the attempts for innovations, the combination of drugs is also under trials. Therefore, we used the density functional theory method and quantum theory of atoms in molecules to investigate drug-drug interactions involving Remdesivir and Favipiravir. The computed parameters were related to the antiviral actions of both drugs together. The results indicate enhanced antiviral activity and it will be worthy to consider additional investigations with the combination of these two drugs.

Theoretical study of the interactions between peptide tyrosine tyrosine [PYY (1-36)], a newly identified modulator in type 2 diabetes pathophysiology, with receptors NPY1R and NPY4R

PURPOSE

Diabetes mellitus is a common condition in the clinically obese. Bariatric surgery is one of the ways to put type 2 diabetes in remission. Recent findings propose the appetite-regulator peptide tyrosine tyrosine (PYY) as a therapeutic option for patients with type 2 diabetes. This novel gut hormone restores impaired insulin and glucagon secretion in pancreatic islets and is implicated in type 2 diabetes reversal after bariatric surgery. The current study elucidates the interactions between PYY and the NPY1R and NPY4R receptors using computational methods.

METHODS

Protein structure prediction, molecular docking simulation, and molecular dynamics (MD) simulation were performed to elucidate the interactions of PYY with NPY1R and NPY4R.

RESULTS

The predicted binding models of PYY-NPY receptors are in agreement with those described in the literature, although different interaction partners are presented for the C-terminal tail of PYY. Non-polar interactions are predicted to drive the formation of the protein complex. The calculated binding energies show that PYY has higher affinity for NPY4R (ΔG_GBSA = -65.08 and ΔG_PBSA = -87.62 kcal/mol) than for NPY1R (ΔG_GBSA = -23.11 and ΔG_PBSA = -50.56 kcal/mol).

CONCLUSIONS

Based on the constructed models, the binding conformations obtained from docking and MD simulation for both the PYY-NPY1R and PYY-NPY4R complexes provide a detailed map of possible interactions. The calculated binding energies show a higher affinity of PYY for NPY4R. These findings may help to understand the mechanisms behind the improvement of diabetes following bariatric surgery.

Virtual screening, ADMET profiling, PASS prediction, and bioactivity studies of potential inhibitory roles of alkaloids, phytosterols, and flavonoids against COVID-19 main protease (Mpro)

The current research used a virtual screening method to study 57 isolated phytochemicals (alkaloids, phytosterols, and flavonoids) against the SARS-CoV-2 main protease (M^pro). The absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the selected compounds were analysed using admetSAR tool while SwissADME and Molinspiration chemoinformatics tools were used to examine the oral bioavailability and drug-likeness properties. Parameters such as physicochemical properties, activity spectra for substances (PASS) prediction, bioactivity, binding mode, and molecular interactions were also analysed. Our results favoured Lupeol (-8.6 kcal/mol), Lupenone (-7.7 kcal/mol), Hesperetin (-7.4 kcal/mol), Apigenin (-7.3 kcal/mol) and Castasterone (-7.3 kcal/mol) as probable inhibitors of SARS-CoV-2. This is because of their good binding affinities, bioactivities, drug-likeness, ADMET properties, PASS properties, oral bioavailability, binding mode and their interactions with the active site of the target receptor compared to Remdesivir and Azithromycin. Therefore, these compounds could be explored towards the development of new therapeutic agents against SARS-CoV-2.

2,4-Dimorpholino-4-yl-6-(4-nitrophenoxy)-[1,3,5]-triazine: Structural and spectroscopic study using experimental and DFT method

2,4-Dimorpholino-4-yl-6-(4-nitrophenoxy)-[1,3,5]-triazine (DMNT) was synthesized and the molecular structure and vibrational frequencies were studied by density functional theory (DFT) method. The functional used was Becke’s three parameter exchange functional combined with the Lee-Yang-Parr correlation (B3LYP) and the standard basis set was 6-31G(d) for all atoms. The Fourier Transform-Infra Red (FT-IR) and FT-Raman spectra of DMNT were recorded and complete assignments of the observed vibrational frequencies are done. The assignments were confirmed by isotopic labelling. The structural parameters, harmonic vibrational frequencies, IR intensities and Raman intensities of DMNT in the ground-state were also computed. Non-linear optical behaviour of DMNT was analysed by examining the properties like electric dipole moment, polarizability and hyperpolarizability. Molecular properties such as ionization potential, electro-negativity, chemical potential and chemical hardness were obtained from molecular orbital analysis. Hyper conjugative interaction and charge delocalization taking place in DMNT was confirmed by Natural bond analysis studies. UV-Vis spectrum of DMNT was also recorded to understand the electronic properties.

Graphical Abstract:

BiCl3-Facilitated removal of methoxymethyl-ether/ester derivatives and DFT study of –O–C–O– bond cleavage

An experimental and DFT study of the cleavage of the MOM group mediated by an eco-friendly reagent, bismuth trichloride.

Structural and spectroscopic properties of 3-halogenobenzaldehydes: DFT and TDDFT simulations

Conformers of 3-halogenobenzaldehydes (3HB, halogen atom: F [3FB], Cl [3CB] and Br [3BB]) in the gas phase and solutions were studied using density functional theory (DFT) and time dependent density functional theory (TDDFT), B3LYP functional and MP2 method with 6–311+G(3df,p) and aug-cc-pVDZ basis sets. The present study aims to investigate the halogen and medium effects on the conformational stability, structural parameter, dipole moment, carbonyl stretching frequency, frontier molecular orbitals, band gap, absorption band and density of states. Carbonyl stretching frequencies were evaluated with some solvent models. All results will be useful for further analysis of halogen-substituted benzaldehydes.

Spectroscopic and DFT studies of 2,4-dichloro-N-phenethylbenzenesulfonamide

The Fourier-transform infrared spectroscopy (FT-IR) spectrum of 2,4-dichloro-N-phenethylbenzenesulfonamide (DPBS) was obtained and the compound was studied theoretically. The optimized geometry, total electronic energy and vibrational wavenumbers of DPBS were examined using Hartree–Fock (HF) and density functional theory (DFT) method such as B3LYP, BP86 and M06 functionals with the basis set of 6-311++G(d,p) for all atoms. A complete vibrational assignment was studied for DPBS. The molecular orbital energies, polarizability and thermodynamic properties of DPBS were also computed. Analysis of molecular orbitals reveals the parameters such as chemical potential, chemical hardness and electrophilicity index. The molecular properties such as electric dipole moment µ, polarizability α, and hyperpolarizability β reveal the non-linear optical (NLO) property of DPBS. Natural bond analysis study reveals charge delocalization of the molecule. The experimental and computational results are found to have good agreement among themselves. The results of this work will pave the way for further insight in the study of the applications of DPBS.

Graphical Abstract:

Theoretical Study of the Microhydration the Chemical Warfare Agent Sulfur Mustard

A microhydration study of sulfur mustard (SM) was carried out using M06-2X, B3LYP, B3LYP-D3, and MP2 levels of theory with the 6-311++G(2d,2p) basis set. The changes in energetics, structural parameters and vibrational wavenumbers following the addition of up to three discrete water molecules to SM were analyzed. We observed slight changes in the geometry of SM upon microhydration. The stability of hydrated clusters is due to weak C-H···O-H hydrogen bonds. The free energy change for the formation of the clusters is positive at room temperature and becomes exergonic when the temperature decreases. The infrared stretchings of C-Cl of SM and O-H of water are redshifted upon the addition of water molecules. The findings from this work add to the literature of hydrated SM and can be useful in its detection and subsequent destruction.

Correction: A colorimetric probe for the real-time naked eye detection of cyanide and hydroxide ions in tap water: experimental and theoretical studies

Correction for ‘A colorimetric probe for the real-time naked eye detection of cyanide and hydroxide ions in tap water: experimental and theoretical studies’ by Veikko Uahengo et al., Analyst, 2019, 144, 6422–6431.

A theoretical study of the hydrolysis mechanism of A-234; the suspected novichok agent in the Skripal attack

A-234, [EtO–P( Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O)(F)–NC(Me)–N(Et)₂], is the suspected A-type nerve agent used in the Skripal attack on the 4th of March 2018. Studies related to the structure and reactivity of this compound are limited. We, therefore, aimed at understanding the underlying hydrolysis mechanism of A-234 within the DFT framework. The attack of the water molecule can occur at the phosphinate and acetoamidine reactive centres. Our theoretical findings indicate that the hydrolysis at the acetoamidine centre is thermodynamically favoured compared to the hydrolysis at the phosphinate centre. The hydrolysis at the acetoamidine moiety may proceed via two pathways, depending on the nitrogen atom participating in the hydrolysis. The main pathway consists of four distinct channels to reach the final product, with the concerted 1,3-proton shift favoured kinetically and thermodynamically in the gas phase and water as solvent. The results are in good agreement with the literature, although some differences in the reaction mechanism were observed.

A theoretical study of the hydrolysis mechanism of A-234 [EtO–P(O)(F)–NC(Me)–N(Et)₂]; the suspected novichok agent in the Skripal attack.

Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN 2 Reaction of NH 2 - and CH3 Cl

We have computationally studied the bimolecular nucleophilic substitution (S_N 2) reactions of M_n NH₂ ^(n-1) + CH₃ Cl (M⁺  = Li⁺ , Na⁺ , K⁺ , and MgCl⁺ ; n = 0, 1) in the gas phase and in tetrahydrofuran solution at OLYP/6-31++G(d,p) using polarizable continuum model implicit solvation. We wish to explore and understand the effect of the metal counterion M⁺ and of solvation on the reaction profile and the stereochemical preference, that is, backside (S_N 2-b) versus frontside attack (S_N 2-f). The results were compared to the corresponding ion-pair S_N 2 reactions involving F^- and OH^- nucleophiles. Our analyses with an extended activation strain model of chemical reactivity uncover and explain various trends in S_N 2 reactivity along the nucleophiles F^- , OH^- , and NH 2 - , including solvent and counterion effects. © 2019 Wiley Periodicals, Inc.

A colorimetric probe for the real-time naked eye detection of cyanide and hydroxide ions in tap water: experimental and theoretical studies

Herein, a colorimetric sensor (L) based on a naphthyl derivative bearing hydrazone receptors was synthesized via a one-step reaction process, and its recognition properties towards biologically important anions in an acetonitrile-water mixture were investigated by naked-eye observation and UV-Vis and ¹H NMR spectroscopy. The molar addition of anions, such as TBAF^-, TBAOH^-, TBACN^- and TBAAcO^-, induced a significant red shift in the charge transfer band (Δλ = 73 nm, from 337 nm to 410 nm), in agreement with visible "naked eye" detectable colorimetric activities; in addition, soaked-in-L paper strips were prepared, which could significantly discriminate cyanide (KCN) and hydroxide (NaOH) ions dissolved in tap water via the litmus test method. This study was complemented by density functional theory computations to gain more insight into the interaction between L and anions.

"Smart" Triiodide Compounds: Does Halogen Bonding Influence Antimicrobial Activities?

Antimicrobial agents containing symmetrical triiodides complexes with halogen bonding may release free iodine molecules in a controlled manner. This happens due to interactions with the plasma membrane of microorganisms which lead to changes in the structure of the triiodide anion. To verify this hypothesis, the triiodide complex [Na(12-crown-4)2]I3 was prepared by an optimized one-pot synthesis and tested against 18 clinical isolates, 10 reference strains of pathogens and five antibiotics. The antimicrobial activities of this symmetrical triiodide complex were determined by zone of inhibition plate studies through disc- and agar-well-diffusion methods. The triiodide complex proved to be a broad spectrum microbicidal agent. The biological activities were related to the calculated partition coefficient (octanol/water). The microstructural analysis of SEM and EDS undermined the purity of the triiodide complex. The anionic structure consists of isolated, symmetrical triiodide anions [I-I-I]- with halogen bonding. Computational methods were used to calculate the energy required to release iodine from [I-I-I]- and [I-I···I]-. The halogen bonding in the triiodide ion reduces the antibacterial activities in comparison to the inhibitory actions of pure iodine but increases the long term stability of [Na(12-crown-4)2]I3.

Molecular structure and vibrational spectra of 2-(4-bromophenyl)-3-(4-hydroxyphenyl) 1,3-thiazolidin-4-one and its selenium analogue: Insights using HF and DFT methods

2-(4-Bromophenyl)-3-(4-hydroxyphenyl)-1,3-thiazolidin-4-one and its selenium analogue were studied in the gas phase using HF and DFT methods. The functionals considered were B3LYP, BP86 and M06. The basis set for all the atoms was 6-311++ G(d,p). Molecular parameters such as bond lengths, bond angles, rotational constants, dipole moments, electronic energies, and vibrational parameters namely harmonic vibrational frequencies and relative intensities were computed for these compounds. Atomization energies, HOMO-LUMO gaps and natural charges on the atoms were also calculated. The molecular parameters and the vibrational spectra of sulfur compound are in good agreement with the experimental data. Therefore, the data for the selenium analogue should be helpful in its future characterization.

Theoretical study of the molecular aspect of the suspected novichok agent A234 of the Skripal poisoning

Novichoks are the suspected nerve agents in the March 2018 Skripal poisoning. In this context, the novichok agent A234 (chemical structure proposed by Mirzayanov) was studied using computational methods to shed light on its molecular, electronic, spectroscopic, thermodynamic and toxicity parameters as well as on potential thermal and hydrolysis degradation pathways. The poisoning action and antidote of A234 were also investigated. Some of these parameters were compared to three common G- and V-series nerve agents, namely GB, VR and VX. The research findings should be useful towards the detection, development of antidotes and destruction of A234.

Theoretical investigation of the derivatives of favipiravir (T-705) as potential drugs for Ebola virus

Density functional theory (DFT) method was used to compute the structural and vibrational parameters of favipiravir (T-705) in the gas phase. The functional used was B3LYP in conjuction with the 6–311++G(d,p) basis set. We also computed these parameters for unsubstituted T-705 and derivatives of T-705 by substituting fluorine by chlorine, bromine and the cyanide group. There is a good comparison between the computed and experimental parameters for T-705 and therefore, the predicted data should be reliable for the other compounds for which experimental data is not available. We extended our DFT study to include molecular docking involving the Ebola virus viral protein 35 (VP35). The docking results indicate that the T-705 and its chlorine and bromine analogues have comparable free energy of binding with VP35.

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