Introducing “UCA-FUKUI” software: reactivity-index calculations

Investigation of the reactivity indices for the formation of substituted dinitroanilines and correlations to their dockings on α-tubulin of Plasmodium falciparum

The local and global reactivity descriptors of substituted dinitroaniline analogues were investigated using M06-2X/6-31 + G(d,p) method. It was observed that NH₂ (m = 3.53 eV; p = 3.70 eV) substituent conveyed the highest nucleophilic character on the benzene ring system than the other groups under study. For the substrates 4-substituted-1-chloro-2,6-dinitrobenzenes, the condensed to atom electrophilicity ([Formula: see text]) increases in the order COOCH₃ > NO₂ > F > SO₃H > CN > Cl > Br. The para substituted groups with the halogens follow the order of increasing electronegativity, F > Cl > Br. However, the nucleophilicity of the halo substituents of the products increases in the order, F > Br > Cl. Molecular docking simulations using the homology model with the crystallographic structure of zinc-induced bovine tubulin heterodimer (1JFF) as one of the templates reveal that the interactions between the tubulins of Plasmodium falciparum and dinitroaniline analogues are due to H-bonding. In general, the binding interaction is with the following residues: Met137, ARG64, Lys60, Glu183, Val4, His28, Cys171, Tyr224, Asn206, 228, Ile235, and Leu238. The pK_as of the residue decrease as the ring activating power of the substituents increases from strongly activating to weakly activating groups. There is no evidence of intra or intermolecular H-bonding between Arg64 and Cys171. Electronegativity (χ) gives a better generic description of the dinitroanilines than any other parameters considered. Short-range hydrophobic interaction contributes to reduced binding affinities of the ligands. Graphical abstractReaction of substituted 2,6-dinitro chlorobenzene with diisopropylamine. Orbital interaction between the substrates and diisopropylamine in the formation of the dinitroanilines.

Synthesis of Pyrazolo-Fused 4-Azafluorenones in an Ionic Liquid. Mechanistic Insights by Joint Studies Using DFT Analysis and Mass Spectrometry

A series of pyrazolo-fused 4-azafluorenones (indeno[1,2-b]pyrazolo[4,3-e]pyridines, IPP) were synthesized via the three-component reaction between arylaldehydes, 3-methyl-1H-pyrazol-5-amine and 1,3-indanedione in an ionic liquid as a catalyst at room temperature. The applied synthetic route has the advantages of easy work-up under mild reaction conditions presenting moderate yields and an environmentally benign procedure. A theoretical study based on conceptual-density functional theory has been done, bond reactivity indices have been calculated and an electrophilic and nucleophilic character of localized orbitals has been determined to analyze the possible electronic mechanisms.

Characterization of electrophilicity and oxidative potential of atmospheric carbonyls

Carbonyls are reactive and electrophilic compounds found ubiquitously in the atmosphere. The interactions between atmospheric carbonyls and biological nucleophiles (e.g., thiol-containing compounds) have important implications on their toxicity, but the underlying mechanisms have not been fully understood. In this study, we used combined computational and experimental approaches to assess the reactivities of atmospheric carbonyls in respect to their electrophilic properties. Global electrophilicity indexes (ω) were calculated based on density functional theory. The reactivities of carbonyls with thiols were assessed using the dithiothreitol (DTT) assay as a surrogate of biological nucleophilic antioxidants. The computational results indicated that the ω of a given carbonyl compound is largely influenced by its molecular structure and adjacent functional groups. The calculated ω values showed a strong linear correlation with the logarithm of measured carbonyl mass-normalized DTT consumption rates (r² = 0.8378 and 0.9899 for simple and α,β-unsaturated carbonyls, respectively). The removal of DTT through the nucleophilic addition pathway was confirmed by the detection of carbonyl-DTT adducts using the gas chromatography/electron ionization-mass spectrometry (GC/EI-MS) technique. Our results demonstrated that electrophilicity index can be potentially used as a molecular descriptor to predict toxicity of atmospheric carbonyls towards thiol-containing biomolecules. This work also highlights the significance of carbonyls in interpreting DTT-based aerosol oxidative potential.

New advances in conceptual-DFT: an alternative way to calculate the Fukui function and dual descriptor

An alternative way of calculating the Fukui function and the partial derivative of second order of the electronic density with respect to the number of electrons N is presented, the new formulas agree with the usual ones but only in cases without degeneracy. The new operative formulas are more general than the previous ones and are the right ones for those problematic cases where one or both of the frontier molecular orbitals are degenerate. Finally, we present a new way of applying the finite difference approximation that leads to more realistic results than the usual formulas. Graphical abstract A new way of calculating the Fukui function is presented that results in a new operative formula of the function. It has also been obtained the partial derivative of second order of the electronic density with respect to the number of electrons N, and it agree with the usual formula of the dual descriptor function but only in cases without degeneration.

Triazole-modified chitosan: a biomacromolecule as a new environmentally benign corrosion inhibitor for carbon steel in a hydrochloric acid solution

In this work, a new inhibitor, triazole modified chitosan, was synthesized for the first time following chemical modification of chitosan using 4-amino-5-methyl-1,2,4-triazole-3-thiol. The newly synthesized biopolymer (CS–AMT) was characterized using FTIR and NMR, and then it was evaluated as an inhibitor against corrosion of carbon steel in 1 M hydrochloric acid. The corrosion testing and evaluation were performed thoroughly employing the weight loss method, electrochemical measurements and surface analysis. A maximum corrosion inhibition efficiency of >95% was obtained at 200 mg L⁻¹ concentration of inhibitor. The adsorption of inhibitor obeyed the Langmuir isotherm and showed physical and chemical adsorption. The electrochemical study via impedance analysis supported the adsorption of the inhibitor on the surface of carbon steel, and the potentiodynamic polarization indicated a mixed type of inhibitor behavior with cathodic predominance. To get a better insight on the interaction of inhibitor molecules with the metal surface, a detailed theoretical study was performed using DFT calculations, Fukui indices analysis and molecular dynamics (MD) simulation. The DFT study showed a lower energy gap of CS–AMT and the MD simulations showed an increased binding energy of CS–AMT compared to the parent chitosan and triazole moieties thereby supporting the experimental findings.

A novel derivative of chitosan is evaluated as an environment-friendly corrosion inhibitor for carbon steel in hydrochloric acid solution.

A Predictive Tool for Electrophilic Aromatic Substitutions Using Machine Learning

At the early stages of the drug development process, thousands of compounds are synthesized in order to attain the best possible potency and pharmacokinetic properties. Once successful scaffolds are identified, large libraries of analogues are made, which is a challenging and time-consuming task. Recently, late stage functionalization (LSF) has become increasingly prominent since these reactions selectively functionalize C-H bonds, allowing to quickly produce analogues. Classical electrophilic aromatic halogenations are a powerful type of reaction in the LSF toolkit. However, the introduction of an electrophile in a regioselective manner on a drug-like molecule is a challenging task. Herein we present a machine learning model able to predict the reactive site of an electrophilic aromatic substitution with an accuracy of 93% (internal validation set). The model takes as input a SMILES of a compound and uses six quantum mechanics descriptors to identify its reactive site(s). On an external validation set, 90% of all molecules were correctly predicted.

Microwave-Induced Synthesis of Chitosan Schiff Bases and Their Application as Novel and Green Corrosion Inhibitors: Experimental and Theoretical Approach

Environmentally friendly three chitosan Schiff bases (CSBs) were first time synthesized under microwave irradiation by the reaction of chitosan and aldehydes [benzaldehyde (CSB-1), 4-(dimethylamino)benzaldehyde (CSB-2), and 4-hydroxy-3-methoxybenzaldehyde (CSB-3)] and characterized by IR and NMR spectroscopy. The corrosion inhibition performance of the synthesized inhibitors was studied by the electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization (PDP). The results show that all the Schiff bases (CSBs) act as effective corrosion inhibitors for mild steel in 1 M HCl solution. Among the synthesized Schiff bases, CSB-3 exhibited the maximum inhibition efficiency of 90.65% at a very low concentration of 50 ppm. The EIS results showed that the CSBs inhibit corrosion by the adsorption mechanism. The PDP results show that all the three Schiff bases are mixed-type inhibitors. The formation of inhibitor films on the mild steel surface was supported by scanning electron microscopy/energy dispersive X-ray analysis and Fourier-transform infrared spectroscopy methods. The adsorption of CSBs on the mild steel surface obeys the Langmuir adsorption isotherm. The theoretical studies via density functional theory and molecular dynamics simulation corroborated the experimental results.

Introducing a new bond reactivity index: Philicities for natural bond orbitals

In the present work, a new methodology defined for obtaining reactivity indices (philicities) is proposed. This is based on reactivity functions such as the Fukui function or the dual descriptor, and makes it possible to project the information from reactivity functions onto molecular orbitals, instead of onto the atoms of the molecule (atomic reactivity indices). The methodology focuses on the molecules' natural bond orbitals (bond reactivity indices) because these orbitals have the advantage of being localized, allowing the reaction site of an electrophile or nucleophile to be determined within a very precise molecular region. This methodology provides a "philicity" index for every NBO, and a representative set of molecules has been used to test the new definition. A new methodology has also been developed to compare the "finite difference" and the "frontier molecular orbital" approximations. To facilitate their use, the proposed methodology as well as the possibility of calculating the new indices have been implemented in a new version of UCA-FUKUI software. In addition, condensation schemes based on atomic populations of the "atoms in molecules" theory, the Hirshfeld population analysis, the approximation of Mulliken (with a minimal basis set) and electrostatic potential-derived charges have also been implemented, including the calculation of "bond reactivity indices" defined in previous studies. Graphical abstract A new methodology defined for obtaining bond reactivity indices (philicities) is proposed and makes it possible to project the information from reactivity functions onto molecular orbitals. The proposed methodology as well as the possibility of calculating the new indices have been implemented in a new version of UCA-FUKUI software. In addition, this version can use new atomic condensation schemes and new "utilities" have also been included in this second version.

An impending inhibitor useful for the oil and gas production industry: Weight loss, electrochemical, surface and quantum chemical calculation

The influence of a Schiff base namely N,N'-(pyridine-2,6-diyl)bis(1-(4-methoxyphenyl) methanimine) (PM) on the corrosion of J55 and N80 steel in 3.5 wt.% NaCl solution saturated with CO2 was evaluated using weight loss, potentiodynamic polarization, electrochemical impedance spectroscopy (EIS), X-ray diffraction (XRD), contact angle, scanning electron microscopy (SEM), atomic force microscopy (AFM) and scanning electrochemical microscopy (SECM). Potentiodynamic polarization results suggested that the inhibitor acted as a mixed type inhibitor by reducing both anodic and cathodic reactions. The adsorption of PM on the J55 and N80 steel surface obeyed the Langmuir adsorption isotherm. XRD, contact angle, SEM, AFM and SECM studies revealed that the surface of the metal was quite unaffected after the addition of inhibitor. Quantum chemical calculations and molecular dynamic simulation support the experimental results well.

Synthesis and DFT Calculations of Novel Vanillin-Chalcones and Their 3-Aryl-5-(4-(2-(dimethylamino)-ethoxy)-3-methoxyphenyl)-4,5-dihydro-1H-pyrazole-1-carbaldehyde Derivatives as Antifungal Agents

Novel (E)-1-(aryl)-3-(4-(2-(dimethylamino)ethoxy)-3-methoxyphenyl) prop-2-en-1-ones 4 were synthesized by a Claisen-Schmidt reaction of 4-(2-(dimethylamino)ethoxy)-3-methoxy-benzaldehyde (2) with several acetophenone derivatives 3. Subsequently, cyclocondensation reactions of chalcones 4 with hydrazine hydrate afforded the new racemic 3-aryl-5-(4-(2-(dimethylamino)ethoxy)-3-methoxyphenyl)-4,5-dihydro-1H-pyrazole-1-carbaldehydes 5 when the reaction was carried out in formic acid. The antifungal activity of both series of compounds against eight fungal species was determined. In general, chalcone derivatives 4 showed better activities than pyrazolines 5 against all tested fungi. None of the compounds 4a–g and 5a–g showed activity against the three Aspergillus spp. In contrast, most of the compounds 4 showed moderate to high activities against three dermatophytes (MICs 31.25–62.5 µg/mL), being 4a followed by 4c the most active structures. Interestingly, 4a and 4c possess fungicidal rather than fungistatic activities, with MFC values between 31.25 and 62.5 μg/mL. The comparison of the percentages of inhibition of C. neoformans by the most active compounds 4, allowed us to know the role played by the different substituents of the chalcones’ A-ring. Also the most anti-cryptococcal compounds 4a–c and 4g, were tested in a second panel of five clinical C. neoformans strains in order to have an overview of their inhibition capacity not only of standardized but also of clinical C. neoformans strains. DFT calculations showed that the electrophilicity is the main electronic property to explain the differences in antifungal activities for the synthesized chalcones and pyrazolines compounds. Furthermore, a quantitative reactivity analysis showed that electron-withdrawing substituted chalcones presented the higher electrophilic character and hence, the greater antifungal activities among compounds of series 4.

Understanding the regioselectivity of Michael addition reactions to asymmetric divinylic compounds

In the present paper, we describe the synthesis of novel monomers prepared by regioselective Michael addition to asymmetric divinylic compounds.

Synthesis, Characterisation, and in Vitro Antibacterial Evaluation of a New Class of 2-substituted-4-methyl-7,8-dihydro-5H-pyrimido[4,5-d]thiazolo[3,2-a] Pyrimidines

The reaction of 2,4-dichloro-5-(chloromethyl)-6-methylpyrimidine with 4,5-dihydrothiazol-2-amine in chloroform led to the formation of 2-chloro-4-methyl-7,8-dihydro-5H-pyrimido[4,5-d]thiazolo[3,2-a]pyrimidine (3). The true structure of the target compound was confirmed by density functional theory calculations of condensed Fukui indices. The substitution of the 2-Cl function in compound 3 with different secondary amines yielded 2-substituted-4-methyl-7,8-dihydro-5H-pyrimido[4,5-d]thiazolo[3,2-a]pyrimidines in good yields. The assigned products were tested for their potential antibacterial activity and the results indicated that a few derivatives are valuable compounds with great potential to be used as antibacterial agents.

Synthesis of New Derivatives of Pyridazino[6,1-c]Pyrimido[5,4-e][1,2,4]Triazine; a Novel Heterocyclic System

Several derivatives of the novel pyridazino[6,1-c]pyrimido[5,4-e][1,2,4]triazine ring system have been synthesised through heterocyclisation of 5-bromo-2,4-dichloro-6-methylpyrimidine with 3-chloro-6-hydrazinylpyridazine followed by treatment with secondary amines in boiling ethanol.

Reactivity indices for natural bond orbitals: a new methodology

A new reactivity index has been defined; this parameter is focused on a molecule's natural bond orbitals (NBOs) and derives in a natural way from Fukui functions. NBOs have the advantage of being very localized, allowing the reaction site of an electrophile or nucleophile to be determined within a very precise molecular region. Finally, the indices for a representative set of organic molecules were calculated and their usefulness tested on some protonation reactions.