Does the radical GPRI strongly depend on the population scheme? A comparative study to predict radical attack on unsaturated molecules with the radical general-purpose reactivity indicator.

The reactivity of 22 unsaturated molecules undergoing attack by a methyl radical (⋅CH3) have been elucidated using the condensed radical general-purpose reactivity indicator (condensed radical GPRI) appropriate for relatively nucleophilic or electrophilic molecules. Using the appropriate radical GPRI equation for electrophilic attack or nucleophilic radical attack, seven different population schemes were used to assign the most reactive atoms in each of the 22 molecules. The results show that the condensed radical GPRI is sensitive to the population scheme chosen, but less sensitive than the radical Fukui function. Therefore, the reliability of these methods depends on the population scheme. Our investigation indicates that the condensed radical GPRI is most accurate in predicting the dominant products of the methyl radical addition reactions on a variety of unsaturated molecules when the Hirshfeld, Merz-Singh-Kollman, or Voronoi deformation density population schemes are used. Furthermore, for all populations schemes in the majority of instances where the radical Fukui function failed the radical GPRI was able to identify the most reactive atom under certain reactivity conditions.

Spectroscopic, computational, cytotoxicity, and docking studies of 6-bromobenzimidazole as anti-breast cancer agent.

6-Bromobenzimidazole (6BBZ) has been calculated in this study utilizing the 6-311++G(d,p) basis set and the Becke-3-Lee-Yang-Parr density functional approaches. The basic frequencies and geometric optimization are known. FTIR, FT-Raman, and UV-Vis spectra of the substance are compared between its computed and observed values. The energy gap between highest occupied molecular orbital-lowest unoccupied molecular orbital and molecule electrostatic potentials has been represented by charge density distributions that may be associated with the biological response. Time-dependent density functional theory calculations in the gas phase and dimethyl sulfoxide were carried out to ascertain the electronic properties and energy gap values using the same basis set. Molecular orbital contributions are investigated using the overlap population, partial, and total densities of states. Natural bond analysis was found to have strong electron delocalization by means of π(C4-C9) → π*(C5-C6), LP (N1) → π*(C7-C8), and LP(Br12) → π*(C5-C6) interactions. The Fukui function and Mulliken analysis have been explored on the atomic charges of the molecule. The nuclear magnetic resonance chemical shifts for 1 H and 13 C have been computed using the gauge-independent atomic orbital technique. With the highest binding affinity (-6.2 kcal mol-1 ) against estrogen sulfotransferase receptor (PDB ID: 1AQU) and low IC50 value of 17.23 µg/mL, 6BBZ demonstrated potent action against the MCF-7 breast cancer cell line. Studies on the antibacterial activity and ADMET prediction of the molecule have also been carried out.

Proton-Coupled Electron Transfer and Hydrogen Tunneling in Olive Oil Phenol Reactions.

Olive oil phenols are recognized as molecules with numerous positive health effects, many of which rely on their antioxidative activity, i.e., the ability to transfer hydrogen to radicals. Proton-coupled electron transfer reactions and hydrogen tunneling are ubiquitous in biological systems. Reactions of olive oil phenols, hydroxytyrosol, tyrosol, oleuropein, oleacein, oleocanthal, homovanillyl alcohol, vanillin, and a few phenolic acids with a DPPH• (2,2-diphenyl-1-picrylhydrazyl) radical in a 1,4-dioxane:water = 95:5 or 99:1 v/v solvent mixture were studied through an experimental kinetic analysis and computational chemistry calculations. The highest rate constants corresponding to the highest antioxidative activity are obtained for the ortho-diphenols hydroxytyrosol, oleuropein, and oleacein. The experimentally determined kinetic isotope effects (KIEs) for hydroxytyrosol, homovanillyl alcohol, and caffeic acid reactions are 16.0, 15.4, and 16.7, respectively. Based on these KIEs, thermodynamic activation parameters, and an intrinsic bond orbital (IBO) analysis along the IRC path calculations, we propose a proton-coupled electron transfer mechanism. The average local ionization energy and electron donor Fukui function obtained for the phenolic compounds show that the most reactive electron-donating sites are associated with π electrons above and below the aromatic ring, in support of the IBO analysis and proposed PCET reaction mechanism. Large KIEs and isotopic values of Arrhenius pre-exponential factor AH/AD determined for the hydroxytyrosol, homovanillyl alcohol, and caffeic acid reactions of 0.6, 1.3, and 0.3, respectively, reveal the involvement of hydrogen tunneling in the process.

Spectroscopic, quantum chemical investigation and molecular docking studies on N-(2-benzoylamino) phenyl benzamide: A novel SARS-CoV-2 drug.

The present work describes the structural and spectral properties of N-(2-benzoylamino) phenyl benzamide (NBPB). The geometrical parameters of NBPB molecule such as bond lengths, bond angles and dihedral angles are calculated and compared with experimental values. The assigned vibrational wave numbers are in good agreement with the experimental FTIR and FT Raman spectra. The vibrational frequency of C=O stretching was downshifted to a lower wave number (red shift) due to mesomeric effect. The UV-Vis spectrum of the title compound was simulated and validated experimentally. The energy gap and charge transfer interaction of the title molecule were studied using frontier molecular orbital analysis. The electrophilic and nucleophilic reactivity sites of NBPB were investigated through the analysis of the molecular electrostatic potential surface and the Fukui function. An assessment of the intramolecular stabilization interactions of the molecule was performed using natural bond orbital analysis. The drug-likeness parameter was calculated. To investigate the inhibitory potential of the molecule, molecular docking analysis was conducted against SARS-CoV-2 proteins, revealing its capability to serve as a novel inhibitor against SARS-CoV-2. The high binding affinity of NBPB molecule was due to the presence of hydrogen bonds along with different hydrophobic interactions between the drug and the SARS-CoV-2 protein receptor. Hence, the title molecule is identified to be a potential candidate for SARS-CoV-2.

Computational Studies on the Reactivity of Polycyclic Aromatic Hydrocarbons.

Polycyclic aromatic hydrocarbons (PAHs) are widely present in the environment as toxic pollutants. In this study, quantum chemistry methods are used to study reactions of PAHs in both particle and gas phases. Seven theoretical methods are exploited to predict the reactive sites of 15 PAHs in the particle phase. Among these methods, the performance of the condensed Fukui function (CFF) is optimum. The gas-phase reactions of eight PAHs are also investigated. Except for fluorene, CFF predicts correctly the gas-phase mono-nitro products for seven systems. The products of fluorene predicted by CFF are 1-nitrofluorene and 3-nitrofluorene, which is however inconsistent with the experimental results. Transition state theory is then used to investigate the reaction mechanism of fluorene. Calculated rate constants for 3-nitrofluorene and 2-nitrofluorene formation are much bigger than that for 1-nitrofluorene formation, which is in agreement with the experimental results.

Sulphur vs NH Group: Effects on the CO2 Electroreduction Capability of Phenylenediamine-Cp Cobalt Complexes.

The cobalt complex (I) with cyclopentadienyl and 2-aminothiophenolate ligands was investigated as a homogeneous catalyst for electrochemical CO2 reduction. By comparing its behavior with an analogous complex with the phenylenediamine (II), the effect of sulfur atom as a substituent has been evaluated. As a result, a positive shift of the reduction potential and the reversibility of the corresponding redox process have been observed, also suggesting a higher stability of the compound with sulfur. Under anhydrous conditions, complex I showed a higher current enhancement in the presence of CO2 (9.41) in comparison with II (4.12). Moreover, the presence of only one -NH group in I explained the difference in the observed increases on the catalytic activity toward CO2 due to the presence of water, with current enhancements of 22.73 and 24.40 for I and II, respectively. DFT calculations confirmed the effect of sulfur on the lowering of the energy of the frontier orbitals of I, highlighted by electrochemical measurements. Furthermore, the condensed Fukui function f - values agreed very well with the current enhancement observed in the absence of water.

Protonation of Borylated Carboxonium Derivative [2,6-B10H8O2CCH3]-: Theoretical and Experimental Investigation.

The process of protonation of [2,6-B10H8O2CCH3]- was investigated both theoretically and experimentally. The most suitable conditions for protonation of the derivative [2,6-B10H8O2CCH3]- were found. The process of protonation was carried out in the presence of an excess of trifluoromethanesulfonic acid CF3SO3H at room temperature in dichloromethane solution. The structure of the resulting complex [2,6-B10H8O2CCH3*Hfac]0 was established using NMR data and the results of DFT calculations. An additional proton atom Hfac was found to be localized on one of the facets that was opposite the boron atom in a substituted position, and which bonded mainly with one apical boron atom. The main descriptors of the B-Hfac bond were established theoretically using QTAIM and NBO approaches. In addition, the mechanism of [2,6-B10H8O2CCH3]- protonation was investigated.

Dienophilic reactivity of 2-phosphaindolizines: a conceptual DFT investigation.

The >C=P- or -N=P- functionality in 1,3-azaphospholo[1,5-a]pyridine, named as 2-phosphaindolizine and its 1- and 3-aza derivatives act as dienophiles and undergo Diels-Alder reactions with 1,3-dienes. However, the dienophilic reactivity is affected by the nature of the substituent groups on the two sides of the σ2,λ3-P atom and also by the presence of more nitrogen atom(s) in the five-membered ring. The conceptual density functional theory (DFT) calculations have been used in recent years to predict the reactivity of organic molecules in reactions. We calculated global hardness (η), global softness (S), electronic chemical potential (µ), electrophilicity (ω), and nucleophilicity (N) indices of four classes of 2-phosphaindolizines, on the basis of which their observed relative dienophilic reactivities could be rationalized. Besides, the Fukui functions of the carbon/nitrogen and phosphorus atoms of the >C=P- and -N=P- functionalities were also computed which revealed their hard electrophilic character and accorded well with the dienophilic reactivities observed experimentally. Furthermore, energies and symmetries of the lowest unoccupied molecular orbitals (LUMO) of 2-phosphaindolizines were found to be in conformity with their dienophilic reactivities.

Orbital energies and nuclear forces in DFT: Interpretation and validation.

The bonding and antibonding character of individual molecular orbitals has been previously shown to be related to their orbital energy derivatives with respect to nuclear coordinates, known as dynamical orbital forces. Albeit usually derived from Koopmans' theorem, in this work we show a more general derivation from conceptual DFT, which justifies application in a broader context. The consistency of the approach is validated numerically for valence orbitals in Kohn-Sham DFT. Then, we illustrate its usefulness by showcasing applications in aromatic and antiaromatic systems and in excited state chemistry. Overall, dynamical orbital forces can be used to interpret the results of routine ab initio calculations, be it wavefunction or density based, in terms of forces and occupations.

Spectroscopic characterization, DFT studies, molecular docking and cytotoxic evaluation of 4-nitro-indole-3-carboxaldehyde: A potent lung cancer agent.

The 4-nitro-1H-indole-carboxaldehyde (NICA) molecule was characterized experimentally using FT-IR, FT-Raman and UV-Vis spectra, and it was studied theoretically using DFT calculations. The optimized structure of the NICA molecule was determined by DFT calculations using B3LYP functional with cc-pVTZ basis set. The electron localization function (ELF) and local orbital localizer (LOL) studies were performed to visualize the electron delocalization in the molecule. The experimental and theoretical wavenumbers of the title molecule were assigned using VEDA 4.0 program. The charge delocalization and stability of the title molecule were investigated using natural bond orbital (NBO) analysis. Frontier molecular orbitals (FMOs) and related molecular properties were calculated. UV-Vis spectrum was calculated theoretically and validated experimentally. The reactive sites of the molecule were studied from the MEP surface and Fukui function analysis. The molecular docking analysis reveals that the NICA ligand shows better inhibitory activity against RAS, which causes lung cancer. The in vitro cytotoxic activity of the molecule against human lung cancer cell lines (A549) was determined by MTT assay. Thus, the NICA molecule can be used as a potential candidate for the development of the drug against lung cancer.

Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches.

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm-1 to 2800 cm-1 at 60 K and from 2350 cm-1 to 3250 cm-1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700-3100 cm-1 and 2400-2850 cm-1 at 60 K and 2300-3300 cm-1 and 2300-3200 cm-1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

Rules of Nucleophilic Additions to Zigzag Nanographene Diones*.

Nucleophilic addition of carbon-centered nucleophiles to nanographene ketones represents a valuable late-stage method for the functionalization of zigzag nanographenes, but its use is rare in the chemical literature. Using two model systems, non-Kekulé triangulene-4,8-dione and Kekulé anthanthrone, we identify unexpected regioselectivities and uncover the rules that govern these reactions. Considering the large number of nanographene ketones that have been reported since the pioneering work of Eric Clar, this method enables synthesis and exploration of hitherto unknown functionalized nanographenes.

Analysis of the Gas Phase Acidity of Substituted Benzoic Acids Using Density Functional Concepts.

A theoretical study of the effect of the substituent Z on the gas phase acidity of substituted benzoic acids ZC6H4COOH in terms of density functional theory descriptors (chemical potential, softness and Fukui function) is presented. The calculated gas phase ΔacidG° values obtained were close to the experimental ones reported in the literature. The good relationship between the ΔacidG° values and the electronegativity of ZC6H4COOH and its fragments, suggested a better importance of the inductive than polarizability contributions. The balance of inductive and resonance contributions of the substituent in the acidity of substituted benzoic acids showed that the highest inductive and resonance effects were for the -SO2CF3 and -NH2 substituents in the para- and ortho-position, respectively. The Fukui function confirmed that the electron-releasing substituent attached to the phenyl ring of benzoic acid decreased the acidity in the trend ortho > meta > para, and the electron-withdrawing substituent increased the acidity in the trend ortho < meta < para.

Lewis Acidity and Basicity of Mixed Chlorometallate Ionic Liquids: Investigations from Surface Analysis and Fukui Function.

Mixed chlorometallate ionic liquids (ILs) have been regarded as potential solvents, catalysts, and reagents for many organic processes. The acidity and basicity of these ILs were correlated with theoretically estimated parameters such as electrostatic surface potential maxima and minima, average local surface ionization energy, and Fukui and dual descriptor functions. The introduction of metal chloride into the anions would influence the acidity/basicity of ILs by withdrawing the electron density from the cationic counterpart. For the [C4mim]-based ILs with the mixed-metal anions, the acidity tends to attenuate while the basicity becomes stronger, as compared to the corresponding chloroaluminate ILs. However, the acidity of [(C2H5)3NH]-based ILs with the mixed-metal anions are greater than that of the net chloroaluminate ILs. The Fukui function values showed that most of the mixed chlorometallate ILs belong to bifunctional distribution. The mixed chlorometallate ILs both have electrophilic and nucleophilic sites, which would be beneficial for their applications.

A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin (n = 12-20) clusters.

Theoretical studies are essential for the structural characterization of clusters, when it comes to rationalize their unique size-dependent properties and composition. However, the rapid growth of local minima on the potential energy surface (PES), with respect to cluster size, makes the candidate identification a challenging undertaking. In this article, we introduce a hybrid strategy to explore the PES of clusters. This proposal involves the use of a biased initial population of a genetic algorithm procedure. Each individual in this population is built by assembling small fragments, according to the best matching of the Fukui function. The performance of a genetic algorithm procedure. The performance of the method is assessed on the PES exploration of medium-sized Sin clusters (n = 12-20). The most relevant results are: (a) the method converges at almost half of the time used by the canonical version of the GA and, (b) in all the studied cases, with the exception of Si13 and Si16 , the method allowed to identify the global minimum (GM) and other important low-lying structures. Additionally, the apparent deficiency of the proposal to identify the GM was corrected when a Si atom, or other low-lying isomers, were considered to build the clusters. © 2017 Wiley Periodicals, Inc.

Theoretical Reactivity Study of Indol-4-Ones and Their Correlation with Antifungal Activity.

Chemical reactivity descriptors of indol-4-ones obtained via density functional theory (DFT) and hard-soft acid-base (HSAB) principle were calculated to prove their contribution in antifungal activity [...].

A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules.

By means of the conceptual density functional theory, the so-called dual descriptor (DD) has been adapted to be used in any closed-shell molecule that presents degeneracy in its frontier molecular orbitals. The latter is of paramount importance because a correct description of local reactivity will allow to predict the most favorable sites on a molecule to undergo nucleophilic or electrophilic attacks; on the contrary, an incomplete description of local reactivity might have serio us consequences, particularly for those experimental chemists that have the need of getting an insight about reactivity of chemical reagents before using them in synthesis to obtain a new compound. In the present work, the old approach based only on electronic densities of frontier molecular orbitals is replaced by the most accurate procedure that implies the use of total electronic densities thus keeping consistency with the essential principle of the DFT in which the electronic density is the fundamental variable and not the molecular orbitals. As a result of the present work, the DD will be able to properly describe local reactivities only in terms of total electronic densities. To test the proposed operational formula, 12 very common molecules were selected as the original definition of the DD was not able to describe their local reactivities properly. The ethylene molecule was additionally used to test the capability of the proposed operational formula to reveal a correct local reactivity even in absence of degeneracy in frontier molecular orbitals. © 2016 Wiley Periodicals, Inc.

Insight into the Mechanism of the Michael Reaction.

The mechanism for the nucleophilic addition step of the Michael reaction between methanethiol as a model Michael donor and several α-substituted methyl acrylates (X=F, Cl, Me, H, CN, NO2 ) as model Michael acceptors is described in detail. We suggest a novel way to condense electrophilic Fukui functions at specific atoms in terms of the contributions from the atomic orbitals to the LUMO or, more generally, to the orbital controlling the reaction. This procedure correctly associates activation energies to local electrophilic Fukui indices for the cases treated in this work. The calculated reaction barriers strongly depend on the nature of the substituent. As a general rule, activation energies are governed by structural changes, although electronic factors are significant for electron-withdrawing groups. Nucleophilic addition to Michael receptors is best described as a highly nonsynchronous process, in which the geometry of the transition state comprises a nonplanar six-membered ring. Formation of the S⋅⋅⋅C bond, which defines the interaction between the reactants, progresses ahead of all other primitive processes in the early stages of the transformation. In view of our results, we postulate that highly complex chemical reactions, as is the case for the nucleophilic addition step studied herein, that involve cleavage/formation of a total of six bonds, lower their activation energies by favoring nonsynchronicity, that is, for these types of systems, primitive changes should advance at different rates.

The nucleophilicity of the oxygen functional groups on carbon materials: a DFT analysis.

The nucleophilicity of the five different oxygen functional groups (carboxyl, diketone, ketone, lactone, and quinone) on the graphene are evaluated by DFT calculations. Two different methods are employed to obtain three different reactivity descriptors, namely, sk(-), wk(-), and sk(-)/sk(+). The calculations indicate that the quinone group is the most nucleophilic site among the investigated ones. The diketone and ketone are much less active than the quinone group toward an electrophilic attack. This judgment is further supported by Ag(+)-binding calculations, which mimics an electrophilic attack. In addition, the carboxyl and lactone groups at a zigzag-terminated edge show nucleophilic ability that is comparable to that of diketones. The current work lays the basis for future studies on the redox property of carbon catalysis and its implications in catalytic reactions.

A new strategy to construct MOF-on-MOF derivatives for the removal of tetracycline hydrochloride from water by activation of peroxymonosulfate.

A MOF-on-MOF composite derivative material named ZIF-67@Ce-MOF-600 was designed and synthesized. The preparation of ZIF-67@Ce-MOF-600 was optimized from the aspects of the ratio of metal and ligand, heat-treatment temperature. It was demonstrated by XRD, FT-IR, SEM-EDS and TEM. The optimum conditions for the activation of PMS by ZIF-67@Ce-MOF-600 for the degradation of tetracycline (TC) were investigated by adjusting the catalyst dosage, TC, pH, peoxymonosulfate (PMS) concentration, and different kinds of water, co-existing anions and pollution. Under optimal conditions (20 mg catalysts and 50 mg PMS added) in 100 mL of tetracyclines (TC) solvent (20 mg TC/L), the removal rate could reach up to 99.2% and after five cycles was 70.5%. The EPR results indicated the presence of free radicals and non-free radical, among which free radicals intended to play a major role in the degradation process. Its possible degradation pathways and attack sites were analyzed by liquid-phase mass spectrometry and DFT analysis.