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Amphetamine in fingerprints is predicted to be detectable using fingerprinting reagents by UV-vis spectroscopy and a visible colour change.

Multicobalt(II) two-dimensional layer coordination polymer {[Co(bitbu-OMe)2(NCS)2]·2MeOH}n (1) was synthesized using a bis-imidazole ligand having a steric hindrance, tert-butyl, and one methoxy group expressed by bitbu-OMe (bitbu-OMe = 1,1’-[(5-tert-butyl-2-methoxybenzene-1,3-diyl)dimethanediyl]bis(1H-imidazole). Since there are two methanol molecules trapped inside each void within 1, the investigation of small organic matters removal from organic wastewater was conducted in order to reveal its ability in the purification process. The research findings indicate that 1 has the ability to capture methanol, acetone, acetonitrile, and tetrahydrofuran in organic wastewater with removal ratios of 29.17%, 63.22%, 42.77%, and 21.24%, respectively.

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.

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.

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.

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.

Graphical abstract 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. Supplementary Information The online version contains supplementary material available at 10.1007/s11696-021-01946-8.

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.

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.

We present the results of the analysis of 2,2,6,6-tetramethyl-4-oxo-piperidinium nitrate isolated from the stem bark of

Computational methods were used to analyse the interactions around the metal centres in three transition metal (TM) complexes for which the X-ray data are available. We were particularly interested in understanding the metal–metal interactions. We used concepts of bond order, natural population, quantum theory of atom in molecules, electron localisation functions (ELFs) and non-covalent interactions (NCIs). Our results indicate that these tools can be used effectively to help in having insights into the bonding of TM complexes.

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 (BOD

A simple method for the cleavage of methoxymethyl (MOM)-ether and ester derivatives using bismuth trichloride (BiCl3) is described. The alkyl, alkenyl, alkynyl, benzyl and anthracene MOM ether derivatives, as well as MOM esters of both aliphatic and aromatic carboxylic acids, were deprotected in good yields. To better understand the molecular roles of BiCl3 and water for MOM cleavage, two possible binding pathways were investigated using the density functional theory (DFT) method. The theoretical results indicate the differential initial binding site preferences of phenolic and alcoholic MOM substrates to the Bi atom and suggest that water plays a key role in facilitating the cleavage of the MOM group.

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.

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.

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.

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. © 2019 Walter de Gruyter GmbH, Berlin/Boston 2019., FGA-2019-20390, Authors acknowledge Fencluster system and Scientific Research Projects Coordination Unit of Ege University (Project No: FGA-2019-20390).

The bonding evolution theory has been used to investigate the flow of electron density along the reaction pathways of ethyl acetate 2-oxo-2-(4-oxo-4H-pyrido [1.2-a] pyrimidin-3-yl) polyazaheterocycle (1) and ethylenediamine (2). This reaction has three channels (1-3) and each one takes place via three or four steps. DFT results reveal that channel 2, which goes through imine intermediate is by far the most favorable one, and the main product 3 is more stable than 4 and 5, showing that this reaction is under kinetic and thermodynamic control, in clear agreement with the experimental outcomes. The BET analysis allows identifying unambiguously the main chemical events happening along channel 2. For this reaction channel, the mechanism along the first step (TS2-a) is described by a series of four structural stability domains (SSDs), while five SSDs are required for the second (TS2-b) and the third (TS2-c) one. The first step can be summarized as follow, the appearance of V(N1,C6) basin illustrating the formation of N1-C6 bond (SSD-II), the splitting of N1-H1 bond, followed by 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, consequent of the disappearance of V(C6,O7) basin, the transformation of C6-N1 single bond into double one (SSD-IV). Finally, the appearance of V(O7,H2) basin leading to the elimination of water molecule within the last domain. Overall, for the three reaction steps, the formation of the N-C bond appears always before the O-H one.

Pesticides are chemicals that are used to kill pests. Partition coefficient in n-octanol and water distribution (log Po/w) is one of the useful parameters to understand mobility in biological systems. This chapter consists of a short review of the experimental and computational methods used for the determination of log Po/w. It also includes the application of density functional theory (DFT) method to calculate the log Po/w for 23 pesticides. A comparison of the computed and reported log Po/w of these pesticides resulted in R2 = 0.88, and it improved to 0.96 after excluding two outliers. The findings from this work can be useful to compute log Po/w of novel pesticides.

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.

A new photoredox-catalyzed decarboxylative radical addition approach to functionalized cyclobutanes is described. The reaction involves an unprecedented formal Giese-type addition of C(sp3 )-centered radicals to highly strained bicyclo[1.1.0]butanes. The mild photoredox conditions, which make use of a readily available and bench stable phenyl sulfonyl bicyclo[1.1.0]butane, proved to be amenable to a diverse range of α-amino and α-oxy carboxylic acids, providing a concise route to 1,3-disubstituted cyclobutanes. Furthermore, kinetic studies and DFT calculations unveiled mechanistic details on bicyclo[1.1.0]butane reactivity relative to the corresponding olefin system.

Herein, we describe the synthesis, characterization and computational studies of novel 4-substituted phthalonitriles: (1) 4-(4-((benzothiazole)methyleneamino)phenoxy)phthalonitrile, (2) 4-(4-(3-phenylallylideneamino)phenoxy)phthalonitrile and (3) 4-(4-(4-isopropylbenzylideneamino)phenoxy)phthalonitrile. Compound 1 was obtained from the equimolar condensation reaction of 4-(4-aminophenoxy)phthalonitrile with benzothiazole-2-carboxaldehyde while compounds 2 and 3 were isolated from the reactions of 4-aminophenol with either cinnamaldehyde or cuminaldehyde followed by the nucleophilic substitution reactions of their respective Schiff bases and 4-nitrophthalonitrile. The spectral characterization of 1–3 was done using 1H NMR, IR and UV–Vis spectroscopy, while structural confirmation could be affirmed from single TOF mass spectrometry and single crystal X-ray crystallography (for 1 and 2). Molecular geometry optimizations were conducted using the DFT method and the simulated IR frequencies data concurred well with the experimental data and the respective vibrational assignments. Similarly, TD-DFT studies provided an interesting perspective on the nature of the intra-ligand electronic transitions found within the experimental electronic spectra of the respective Schiff base phthalonitriles. Compound 3 showed the highest Human African sleeping sickness trypanocidal potency.

Scandenone (warangalone) is a flavonoid found in Erythrina species and other plant genera. It has been connected with physiological processes in insects, human cells and bacteria. In this article, an overview of the biological importance of this compound is provided. A detailed analysis of its crystal structure and antibacterial properties were investigated. The experimental study was supplemented using density functional theory (DFT) and quantitative structure-activity relationship (QSAR) methods. Scandenone proved most potent against Mycobacterium smegmatis (mc2 155) with MIC below 1 μg/mL. In general, it was more potent against Gram-positive bacteria. Scandenone may be a potential tuberculosis medication.

The current research used a virtual screening method to study 57 isolated phytochemicals (alkaloids, phytosterols, and flavonoids) against the SARS-CoV-2 main protease (Mpro). 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., Graphical Abstract

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

The purpose of this study was to remove dyes from synthetic dyed wastewater using activated carbon derived from rice husk. The initial dye concentration was 45 mg/L. The batch adsorption worked best in an acidic medium of pH 2, adsorbent dosage of 13 g/L and agitation speed of 100 rpm with maximum dye removal of 80% after 10 min. The maximum adsorption capacity of the absorbent was found to be 2.0 mg/g with a final dye concentration of 10.8 mg/L. The adsorption was found to be a non-spontaneous, endothermic chemisorption process with less disorder which best fitted the Temkin model and followed pseudo-second order. For column adsorption, the highest qo corresponds to 12.8 mg/g and the maximum dye removal was above 99.5%. Some of the experimental deductions were confirmed by gas-phase computations [B3LYP/6-31G(d)].

The proposed SN2 reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles [Ye et al., Org. Lett. 19, 5384–5387 (2017)] were studied theoretically in order to explain the observed stereochemistry of the products. Our computations indicate that the reaction with the aliphatic nucleophile occurs through a backside SN2@P pathway while the reaction with the aromatic nucleophile proceeds through a novel SN2@Cl mechanism, followed by a frontside SN2@C mechanism. To the best of our knowledge, this is the first time that a SN2@Cl mechanism is reported. We also found that on reducing the bulkiness of substituents around the phosphorus atom, the backside SN2@P mechanism is preferred. The conclusions made from investigating the steric effect should help experimentalists to decide for the organophosphorus reactant to achieve the products of desired stereochemistry.

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

A-234, [EtO–P(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.