Dual Descriptor Research Articles

Understanding the origin of reactivity, mechanism and regioselectivity of the [3+2] cycloaddition reaction between nitrile imine and pyrrolopyrazine

AbstractIn this work, we have performed a computational study on the [3+2] cycloaddition (32CA) reaction between nitrile imine and pyrrolopyrazine within molecular electron density theory (MEDT) using B3LYP and M06‐2X DFT functionnals together with 6‐31G(d,p) basis set. This study shows that the popular B3LYP is the appropriate functional for performing this study. The analysis of energy profiles indicates that this 32CA reaction favours kinetically the formation of a single product as observed experimentally. The favour cycloadduct (P1) is formed through a moderate polar stepwise mechanism, in which the first step is the determining one that is characterised by a moderate polarity and the second step by a highly polar character, while the unfavoured one is formed via a nonpolar one‐step asynchronous mechanism. Solvent effects do not change the regioselectivity, but it increases the activation energies. Thermodynamic parameters analysis indicates that this 32CA reaction is characterised by an exothermic and endergonic characters favouring the formation of cycloadduct (P1), as observed experimentally. Conceptual DFT (CDFT) reactivity indices analysis shows that pyrrolopyrazine 2 reacts as a nucleophile, while nitrile imine 3 as an electrophile. Local reactivity descriptors, such as Parr functions and dual descriptors, show that this 32CA reaction is regioselective leading to the formation of P1. Analysis of ELF electron density demonstrated that the interaction between the high electron density reactive centre with that of low electron density leads to the formation of P1 cycloadduct. The obtained results using MEDT method are in great agreement with what observed in the experimental data.

Theoretical calculations of formation and reactivity of o-quinomethide derivatives of resorcin[4]arene with reference to empirical data.

This paper describes theoretical reaction pathways of alkoxybenzyl derivatives of resorcin[4]arene leading to the formation of o-quinomethide derivatives of resorcin[4]arene (o-QMR[4]A). For each case, the activation energies for the formation of one o-QMR[4]A unit and the activation energies for the backward reaction were calculated. Based on the calculated reaction pathways, the reaction mechanism of o-QMR[4]A formation was proposed. Using the example of o-QMR[4]A generated from a methoxy derivative of resorcin[4]arene, the activation energies with selected nucleophiles were calculated and the reaction mechanisms discussed. Reaction path calculations were performed using the nudged elastic band method and semiempirical extended tight-binding method (GFN2-xTB). Using hydroxybenzyl derivatives of resorcin[4]arene as an example, a comparison of calculated activation energies by selected density-functional theory methods with GFN2-xTB and B97-3c geometries was performed. B97-3c and wB97XD methods were used to calculate the energies of the reactants (R), transition states (TS) and products (P) of the analysed reactions. Theoretical reaction mechanisms were discussed with respect to the orbital-weighted Fukui dual descriptor (Δfw) and experimental data.

Experimental and Theoretical Assessments on Anticorrosion Performance of 2-(1H-benzimidazol-2-yl)-3-(4-hydroxyphenyl) Acrylonitrile for Copper in 1M HNO3

The present study was designed to determine the inhibition effect of 2-(1H-benzimidazol-2-yl)-3-(4-hydroxyphenyl) acrylonitrile in 1M HNO3 using a combined experimental and theoretical approach. Mass loss techniques revealed that 2-(1H-benzimidazol-2-yl)-3-(4-hydroxyphenyl) acrylonitrile inhibition efficiency is dependent on its concentration and temperature. It has been shown that the studied molecule inhibits copper corrosion by an adsorption behavior by donating and accepting electrons. Kinetic parameters have been determined and discussed. Quantum chemical parameters calculated by means of density functional theory (DFT) have shown that studied molecule reactivity is strongly related to the electronic properties, which could help to understand the molecule-metal interactions. The reactive sites have been determined by means of Fukui Functions and dual descriptor. Quantitative structure-property relationship (QSPR) model introduced in this study was used to find a set of quantum chemical parameters capable of correlating the experimental and theoretical data in order to design more suitable organic corrosion inhibitors. The theoretically obtained results were found to be consistent with the experimental data reported.

From Density Functional Theory to Conceptual Density Functional Theory and Biosystems.

The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.

Unveiling the Origin of the Selectivity and the Molecular Mechanism in the [3+2] Cycloaddition Reaction of N-aryl-C-carbamoylnitrone with N-arylitaconimide

The [3+2] cycloaddition reaction of N-aryl-C-carbamoylnitrone (nitrone 1) with N-arylitaconimide (ethylene 2) was computationally studied using the B3LYP/6-31G(d) level of theory. An analysis of the different energetic profiles and the transition states’ optimized structures clearly indicated that this 32CA occurred through a non-polar, asynchronous, one-step mechanism, favoring the formation of the ortho–endo cycloadduct, as observed experimentally. The analysis of the reactivity indices derived from the conceptual DFT explains well the low polarity of this 32CA reaction. Parr functions and a dual reactivity descriptors analysis correctly explained the regioselectivity ortho of this 32CA reaction. Solvent effects did not modify the obtained selectivity but it increased the activation energies and decreased the exothermic character of this 32CA reaction. A thermodynamic parameters analysis indicated that this 32CA wascharacterized by an ortho regioselectivity and endostereoselectivity and exothermic and exergonic characters.

Novel insights into formation mechanism of organic chloramines from pre-oxidized algae-laden water: Multiple roles of dissolved organic nitrogen.

Organic chloramines posed significant risks to drinking water safety. However, the formation mechanism of algae-derived organic chloramines remained unclear. In this study, it was observed that pre-oxidation of algal suspensions increased organic chloramine formation during chlorination. Compared to KMnO4 pre-oxidation, O3 significantly increased the organic chloramine formation potential of algal suspensions. Characterization was performed with size exclusion chromatography-multiple detectors (SEC-MDs) to better understand the organic chloramine formation mechanism. The results revealed that low molecular weight proteins (AMW ≤ 0.64 kDa) were the main precursors of organic chloramines after conventional water treatment processes. We then focused on 14 essential amino acids involved in protein formation. Their concentrations and organic chloramine formation potentials were determined, based on which the theoretical organic chloramine formation potentials of the studied samples were evaluated. However, dramatic gaps between theoretical and experimental organic chloramine formations were observed, which suggested that not all organic nitrogen could react with chlorine to form organic chloramine. The condensed dual descriptor (CDD) was calculated to predict the electrophilic substitution reaction sites on peptides. Furthermore, the activation barrier of each proposed reaction was computed to confirm that the reaction sites for chlorine were located on amino groups. This study clarified the formation mechanism of algal-derived organic chloramines, which could provide a powerful theoretical foundation for controlling organic chloramine formation in drinking water processes.

Introducing a new model based on electronegativity equalization principle for the analysis of the natural bond orbital reactivity in the c‐DFT background

AbstractPrevious studies presented two independent models based on the equalization of electronegativity and on an alternative operative formula for the Fukui function. The current paper presents modifications to these models to obtain a new model for calculating the local energy derivatives (electronic chemical potential, local electronic hardness and local hypersoftness) and density (Fukui and dual descriptor indices) in natural bond orbitals for the study of chemical reactivity from the perspective of these orbitals (local electrophilicity and local maximum charge variation have also been deduced). We have radically changed the way of partitioning the electron density because the atomic model cannot distinguish between bonding and non‐bonding electron pairs, or between electrons with different types of bonds, however, this is possible with the model based on bond orbitals. In this respect, this model is ideal for organic reactions because of their correspondence with Lewis structures, which are simple but very useful for representing reaction mechanisms.

Prediction of •OH-Initiated and •NO3-Initiated Transformation Products of Polycyclic Aromatic Hydrocarbons by Electronic Structure Approaches.

The abiotic reaction products of polycyclic aromatic hydrocarbons (PAHs) with hydroxyl radicals (•OH) and nitrate radicals (•NO3) are nitro-, oxygen-, and hydroxyl-containing PAHs (NPAHs, OPAHs, and OHPAHs). Four methods of the highest occupied molecular orbital (HOMO), Fukui function (FF), dual descriptor (DD), and population of π electrons (PP-π) are selected to predict the chemical reactivity of PAHs attacked by •OH and •NO3 in this study. The predicted •OH-initiated and •NO3-initiated transformation products are compared with the main PAH transformation products (PAH-TPs) observed in the laboratory. The results indicate that PP-π and DD approaches fail to predict the transformation products of fused PAHs containing five-membered rings. By predicting the PAH-TPs of 13–14 out of the 15 parent PAHs accurately, HOMO and FF methods were shown to be suitable for predicting the transformation products formed from the abiotic reactions of fused PAHs with •OH and •NO3.

Three-Dimensional Quantitative Structure and Activity Relationship of Flavones on Their Hypochlorite Scavenging Capacity.

Flavonoids, a class of polyphenolic substances widely present in the plant realm, are considered as ideal hypochlorite scavengers. However, to our knowledge, little study has focused on the structure-activity relationship between flavonoids and hypochlorite scavenging capacity. Herein, we report for the first time the three-dimensional quantitative structure and activity relationship (3D-QSAR) combined with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Four models derived from CoMFA and CoMSIA with different combinations of descriptors were built and compared; the CoMFA model, which included both steric and electrostatic fields, showed great potential (R2 = 0.989; Q2 = 0.818) in predictive quality according to both internal and external validation criteria. Additionally, the average local ionization energy (ALIE), electrostatic potential (ESP), and orbital weighted dual descriptor (OWDD) were determined to identify the key structural moiety for scavenging capacity of flavonoids against hypochlorite. The computational results indicated that hypochlorous acid (HClO) serves as an electrophile undergoing electrophilic addition to the C6 carbon, which has the highest negative charge density, which are influenced by the functional groups on the flavones. The DFT calculated mechanism revealed the catalytic role of water of mono- and di-chlorination reactions, characterized by low activation barriers, and the involvement of neutral, instead of high-energy carbocation, intermediates.

Molecular structure, vibrational spectroscopy (FT-IR, Raman), solvent effects, molecular docking and DFT studies of 1-(4-chlorophenyl)-3-(4-ethoxyphenyl)-prop-2-en-1-one

In this present work, a chalcone derivative 1-(4-Chlorophenyl)-3-(4-ethoxyphenyl)-prop-2-en-1-one is investigated using the density functional theory. PES scan is used to find the most stable conformational structure of the title compound. The geometrical parameters, FT-IR and FT-Raman spectra are performed by the DFT method with B3LYP/6-311+G basis set, which are very comparable with the experimental results. UV-Vis spectrum, frontier molecular orbitals, global reactivity descriptors, molecular electrostatic potential surface, NLO parameters and Mulliken charge in the gas phase, various polar and non-polar solvents are performed to reveal solvents effect. Further, it is found that the electronic properties show a good correlation with the polarity of solvents. Hirshfeld Surface analysis demonstrates H···H contact is dominant in the crystal packing. By means of molecular reactivity descriptors such as natural bond orbital analysis, Fukui function and dual descriptor analysis, the chemical reactivity is theoretically estimated. ELF and LOL are used to access the energy density of electrons. Molecular docking illustrates ECC may be a potential inhibitor for 6R3K protein.

Revealing the regioselective N-acylation of 5-bromo-2-aminobenzimidazole using experiment and theoretical calculation

The N-acylation of 2-aminobenzimidazole is widely used in the synthesis of its derivatives, the products exhibit different regioselectivity when reacting with acylation reagents. 5-Bromo-2-aminobenzimidazole was acylated in our laboratory and found the more complex regioselectivity than 2-aminobenzimidazole. When the reaction temperature was at room temperature and using triethylamine as acid acceptor, 5-bromo-2-aminobenzimidazole afford the N-acylation product at primary amine by acyl chloride, while the products at tertiary amines were obtained by di-tert-butyl dicarbonate. To explain this regioselective N-acylation, the double descriptor (DD), condensed dual descriptor (CDD) of 5-bromo-2-aminobenzimidazole and molecular electrostatic potential (MEP) of reactants were calculated. The possible N-acylation paths of the 5-bromo-2-aminobenzimidazole with different acylation agents was studied by density functional theory (DFT) at M062X/def2TZVP//B3LYP-D3/def-SVP level.

Insights into the Mechanism of Ozone Activation and Singlet Oxygen Generation on N-Doped Defective Nanocarbons: A DFT and Machine Learning Study.

N-doped defective nanocarbon (N-DNC) catalysts have been widely studied due to their exceptional catalytic activity in many applications, but the O3 activation mechanism in catalytic ozonation of N-DNCs has yet to be established. In this study, we systematically mapped out the detailed reaction pathways of O3 activation on 10 potential active sites of 8 representative configurations of N-DNCs, including the pyridinic N, pyrrolic N, N on edge, and porphyrinic N, based on the results of density functional theory (DFT) calculations. The DFT results indicate that O3 decomposes into an adsorbed atomic oxygen species (Oads) and an 3O2 on the active sites. The atomic charge and spin population on the Oads species indicate that it may not only act as an initiator for generating reactive oxygen species (ROS) but also directly attack the organics on the pyrrolic N. On the N site and C site of the N4V2 system (quadri-pyridinic N with two vacancies) and the pyridinic N site at edge, O3 could be activated into 1O2 in addition to 3O2. The N4V2 system was predicted to have the best activity among the N-DNCs studied. Based on the DFT results, machine learning models were utilized to correlate the O3 activation activity with the local and global properties of the catalyst surfaces. Among the models, XGBoost performed the best, with the condensed dual descriptor being the most important feature.

Correlating the inhibitory action of novel benzimidazole derivatives on mild steel corrosion with DFT-based reactivity descriptors and MD simulations

The inhibitive action of three novel benzimidazole derivatives namely 2-(2-pyridyl)benzimidazole (B3), 2-bromo-1H-benzimidazole (B2), and 2-chlorobenzimidazole (B1) on mild steel corrosion was investigated using density functional theory (DFT) approach and molecular dynamics simulations (MD). Global reactivity parameters such as the EHOMO, ELUMO, energy gap (ΔE), global softness (σ), electronegativity (χ), electrophilicity index (ω), global hardness (η) and the fraction of electron transferred from the inhibitor to mild steel surface (ΔN) were calculated and discussed with the help of 3–21 G, 6–31 G, 6-31G++ and 6-G++(d,p) methods. Fukui local reactivity indices as well as the dual descriptors were calculated, and the obtained results indicates that all inhibitors molecules have several active sites for both electrophilic and nucleophilic attacks.The adsorption of the molecules under investigation on the Fe (110) surface was quantified using molecular dynamics simulation (MD). The obtained binding energy in both non-protonated and protonated from of the concerned benzimidazole derivatives increases as follows: B3 > B2 > B1, which emphasizes the order of the experimental inhibition effectiveness of the molecules under probe. The formation of bonding and nonbonding interactions in systems of Fe-inhibitors was analyzed by pair correlation function. Our theoretical outcomes were found to be well correlated to the experimental findings earlier reported.

The Dual Descriptor Reveals the Janus-Faced Behaviour of Diiodine.

The Janus–faced ligand behavior of diiodine (I2) was evidenced after applying the dual descriptor (DD or second-order Fukui function), thus providing additional support to the work performed by Rogachev and Hoffmann in 2013. Along with its capacity to reveal sites susceptible to undergo attacks simultaneously of nucleophilic and electrophilic types, another advantage of DD lies in being an orbital-free descriptor. That means it is based only upon total electron densities when written in its most accurate operational formula. This quality is not exclusive of DD because when Fukui functions are written in terms of electron densities instead of densities of frontier molecular orbitals, they become orbital-free descriptors too. Furthermore, the present work is an application of the generalized operational formula of the dual descriptor published in 2016 that takes into account any possible degeneracy in frontier molecular orbitals. As a proof about capabilities of DD, the possible sites for a favorable interaction between I2 with two organometallic compounds [Rh2(O2CCF3)4] and [(C8H11N2)Pt (CH3)] were correctly revealed by overlapping the biggest lobe for receiving nucleophilic attacks of one molecule with the biggest lobe for receiving electrophilic attacks of the other molecule, so allowing to predict the same coordination modes as experimentally known: linear “end–on” for the [(C8H11N2)Pt (CH3)]…I2, and bent “end–on” for the [Rh2(O2CCF3)4]…I2 interactions.

Theoretical spectroscopic electronic elucidation with different solvents (IEFPCM model), biological assessment and molecular docking studies on Moroxydine-Antiviral drug agent

The formational parameter, electron behavior, wave function, and biologic properties of moroxydine molecule are probed using the Gaussian 09 W DFT tool and basis set B3LYP/6–311++G(d,p).The optimized geometrical properties are calculated in gas. For the determination of spectroscopic, vibrational assignments of the title compound, the quantum computation is used. The energy of charge transfer and the molecular interactions are explained by NBO method. From Frontier orbital analysis, energy gap values are determined, the calculation of NLO properties such as dipole moment (μ), linear polarizability (α) and hyper polarizability (β) are done in water, DMSO, methanol and acetone. The UV–Visible spectra are explored using TD-DFT method in the solvents water, DMSO, methanol and acetone. Mullikan’s distribution of charges and the parameters Fukui function, local softness and dual descriptor of the headline compound in gas are calculated. In gas, Electrostatic potential, the wave function’s properties like electron localization function, localized orbital locator and the analysis of intermolecular interaction (NCl), reduced density gradient are determined. Furthermore, the drug likeness mechanism SwissADME is applied to reach the properties of drug likeness. Atlast, a molecular docking study is implemented to look into the title compound for its antiviral activity.

Reactivity and a Charge-Transfer Model Analysis in Aminopolycarboxylic-Metal Complexes.

In the present work, we have calculated several density functional theory (DFT) reactivity descriptors for the aminopolycarboxylate (APC) acids at the B3LYP/6311++G (d,p) levels of theory, aiming to analyze their reactivity. Reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, and condensed Fukui function local indices have been determined to predict the reactivity of APCs. The influence of the solvent was taken into account by employing the CPCM model. The results indicate that the solvation slightly modifies the tendency of the reactivity of the APCs studied. On the other hand, we applied a global and local charge-transfer partitioning model, which introduces two charge-transfer channels [one for accepting electrons (electrophilic) and another for donating one (nucleophilic)] to the complexation reaction of a set of APC acids with transition metals (Mn, Co, and Ni targets enlarged by Fe, Cu, and Zn). The correlation between the charges obtained for the interaction between APC acids and transition metal stability constants provides support for their interpretation as measures of the electrophilicity and nucleophilicity of a chemical species and, at the same time, allows one to describe the donation and back-donation processes in terms of the DFT of chemical reactivity. Also, the application of dual descriptors for these acids provides valuable information concerning the atoms in the reactants playing the most important roles in the reaction, thus helping to improve our understanding of the reaction under study.

Model of B9N9 Response under External Electric Field: Geometry, Electronic Properties, Reaction Activity.

In this paper, we performed the ωB97XD/def2-TZVP method with a density functional theory study on the boron–nitrogen (BN) analogues of cyclo[18]carbon. The geometric structure, polarization properties, and excitation effect were calculated in the presence of an external electric field (EEF). Furthermore, the dual descriptor and Fukui function matrices were employed to predict the tendency towards the electrophilic or nucleophilic reactions of B9N9 under varying EEF strengths. The results show that the application of an EEF will cause the cyclic structure of B9N9 to be considerably distorted towards an elliptical geometry, the polarization to increase, and the reactivity of B9N9 to enhance with the increase in the EEF strength. This is of great significance for further experimental exploration into the catalytic properties of BN fullerenes.

Imidazolium based superalkalis as building block for Lewis base

Inquest for efficient Lewis base an in-silico investigation on NH3 and its structurally similar molecules has been carried out. It has been observed that the ionization energy of the groups attached to the N-centre plays a vital role in determining their stability and reactivity. Among different groups, superalkali ligands make a better Lewis base. Several conceptual DFT descriptors like electrophilicity, nucleophilicity, dual descriptors have been used to analyse the stability and reactivity of the proposed Lewis base. The calculated charge transfer descriptor describes the efficiency of the designed Lewis base to form an adduct with Lewis acid. nc-2e (n = 1,2) AdNDP calculation lends additional support to the bonding of the studied molecules.

Mechanism of ozone adsorption and activation on B-, N-, P-, and Si-doped graphene: A DFT study

• Detailed evolution mechanism of O 3 into ROS on the doped graphene was revealed. • O ads produced from O 3 decomposition was a vital intermediate to generate other ROS. • Types and efficiency of the formed ROS from O ads depended on the doped heteroatoms. • CDD was a useful descriptor for carbonaceous catalyst design based on QSAR model. The detailed evolution mechanism of O 3 into Reactive oxygen species (ROS) is of paramount importance but remains elusive in catalytic ozonation. Herein, we report a density functional theory study to comprehensively reveal the specific evolution processes of O 3 into ROS on the B-, N-, P-, and Si-doped graphene, including the adsorption, decomposition and ROS generation. In contrast to some previous reports that O 3 would directly decompose into effective ROS on catalysts, our results indicate that after O 3 adsorption, the decomposition products are ground state O 2 and the adsorbed oxygen species (O ads ). The O ads is more likely to act as a crucial intermediate for generating other ROS instead of directly attacking the organics. The type of the ROS and generation efficiency vary with the doped heteroatoms, and the heteroatoms of B, P and Si, or the neighboring C of N, would serve as active sites for O 3 adsorption and decomposition. The N- and P-doped graphene are predicted to have the superior performance in ROS generation and catalytic stability. Finally, twenty representative descriptors were adopted to build the quantitative structure–activity relationship (QSAR) with the activation energy barrier of O 3 decomposition. The result indicates that condensed dual descriptor (CDD) could be useful for preliminarily selecting the modified graphene catalysts, since it shows a very good linear relation with the activation energy barrier. This contribution provides an alternative way to gain fundamental insights into the mechanism of catalytic ozonation at the molecular level, and could be helpful for designing more-efficient catalysts in environmental remediation.

DRFD-Net: Using Dual Receptive Field Descriptors for Multitemporal Optical Remote Sensing Image Registration

Multitemporal optical remote sensing image registration is still a challenging problem for current feature-based image registration algorithms due to the complex nonlinear discrepancies arising from diverse factors, including illumination, weather, and surface condition changes. To address the issue, this article attempts to combine the dual receptive field descriptors (DRFDs) constructed by a novel deep convolutional network. In addition, a novel inner loss function (ILF) that imposes constraints on the intermediate descriptors is adopted in order to consolidate the distinguishability of the descriptors when the overlapping areas of the input image patches are large. Subsequently, the dual feature distance maps (DFDMs) are built on the basis of the DRFDs and combined with features from accelerated segment test (FAST) key points for efficient and accurate correspondence establishment across the source image and the target image. Eventually, an iterative algorithm is proposed to remove the possible outliers. Experiments show that the combination of DRFDs trained with the ILF performs better than current learnable local descriptors, such as L2-Net, HardNet, and SOSNet. The image registration results using our method are more accurate than the methods based on learnable descriptors, such as L2-Net, HardNet, and SOSNet, and handcrafted descriptors, such as scale-invariant feature transform (SIFT), SURF, and ORB.