Aromaticity indices, electronic structural properties, and fuzzy atomic space investigations of naphthalene and its aza-derivatives

Tricyclic 1,4-Diphosphinines: Local vs. Global Aromaticity

1D and 2DNICS π . zz SOM ${{{\rm { NICS}}}_{{\rm { {\rm \pi}{}}}{\rm { .zz}}}^{{\rm { SOM}}}}$ (Sigma only model) calculations were performed on recently established tricyclic 1,4-diphosphinines as well as related benzene and pyrazine derivatives. The study was extended to evaluate the effect of the fused rings on the overall aromatic properties with a special focus on functional groups such as carbenes. The effect of non-aromatic heterocycles on the local ring current of the central ring is small, while aromatic heterocycles (e. g. NHC, imidazolium) lead to a global aromaticity. A higher sulfur content of the adjacent five-membered rings reduces the central ring current. The comparison to related tricyclic benzene and pyrazine derivatives showed that the 1,4-diphosphinine systems resemble more closely the situation in the benzene derivatives than the pyrazines. The effect of charged systems was studied using bis(TTF)-fused 1,4-diphosphinines and, according toNICS π . zz SOM ${{{\rm { NICS}}}_{{\rm { {\rm \pi}{}}}{\rm { .zz}}}^{{\rm { SOM}}}}$ values, the neutral form doesn't possess significant aromaticity but the tetracation resembles the global aromatic situation observed for other heterocycles in this study.

A B3LYP-D3 computational study of electronic, structural and torsional dynamic properties of mono-substituted naphthalenes: the effect of the nature and position of substituent

CONTEXT

The effects of selected substituent groups (-CH3, -Br, -CO2CH3, -COOH, and -NH2) and their relative positions on the electronic and structural properties of mono-substituted naphthalenes were investigated theoretically. In order to elucidate the suitability of the studied substituents in different fields including chemistry, spectroscopy, and materials sciences, accurate DFT calculations were performed at the dispersion-corrected B3LYP level of theory (B3LYP-D3/6-311 +  + G(d,p)), and the obtained results were then validated by extensive comparisons with available experimental data. Among the studied substituents, the -NH2 group causes the maximum reduction of the HOMO-LUMO energy gap. This result revealed clearly the suitability of the -NH2 group, compared to other studied substituents, in the chemical synthesis of future organic-semiconductors having small energy gaps. In addition, the level of theory adopted in this study allowed the fine discrimination between the chemical reactivity parameters of the studied congeners, which is very difficult to perform experimentally. On the other hand, the rotational barriers of the studied non-halogen substituent groups were predicted. The greater sensitivity of the rotational barrier heights to the local environments, arising from intra-molecular interactions, was attributed to the -CH3 group. The torsional frequencies, calculated within the harmonic approximation, were also employed to relatively explore the differences between the environments of the same substituent at two different positions. The usefulness of these results can be manifested in the vibrational spectroscopy field, especially, for the IR/ Raman spectral analysis of polycyclic-aromatic congeners.

METHOD

All calculations were conducted within the Density functional theory (DFT) using the so-called dispersion-corrected B3LYP functional (B3LYP-D3) with the carefully selected 6-311 +  + G(d,p) basis set. The B3LYP-D3/6-311 +  + G(d,p) calculations were performed using the Gaussian 09 program, and the obtained results were visualized by employing the GaussView 6.0.16 program.

New flavone-based arylamides as potential V600E-BRAF inhibitors: Molecular docking, DFT, and pharmacokinetic properties

Objectives

The V600E-BRAF protein kinase is an attractive and essential therapeutic target in melanoma and other tumors. However, because of its resistance to the known inhibitors and side effects of some identified inhibitors, new potent inhibitors need to be identified.

Methods

In the present work, in silico strategies such as the molecular docking simulation, DFT (Density-Functional-Theory) computations, and pharmacokinetic evaluation were used to determine potential V600E-BRAF inhibitors from a set of 31 synthesized novel flavone-based arylamides.

Results

The docking result demonstrated that four compounds (10, 11, 28, and 31) had acceptable docking scores (MolDock score of -167.523 kcal mol^-1, -158.168 kcal mol^-1, -160.581 kcal mol^-1,-162.302 kcal mol^-1, and a Rerank score of -124.365, -129.365, -135.878 and -117.081, respectively) appeared as most active and potent V600E-BRAF inhibitors that topped vemurafenib (-158.139 and -118.607 kcal mol^-1). The appearance of H-bonds and hydrophobic interactions with essential residues for V600E-BRAF proved the high stability of these complexes. The energy for the frontier molecular orbitals such as HOMO, LUMO, energy gap, and other reactivity parameters was computed using DFT. The frontier molecular-orbital surfaces and electrostatic potentials (EPs) were investigated to demonstrate the charge-density distributions that might be linked to anticancer activity. Similarly, the chosen compounds revealed superior pharmacological properties according to the drug-likeness rules (bioavailability) and pharmacokinetic properties.

Conclusion

The chosen compounds were recognized as potent V600E-BRAF inhibitors with superior pharmacokinetic properties and could be promising cancer drug candidates.

Deciphering the electrochemical sensing capability of novel Ga12As12 nanocluster towards chemical warfare phosgene gas: insights from DFT

The applications of 3D inorganic nanomaterials in environmental and agriculture monitoring have been exploited continuously; however, the utilization of semiconductor nanoclusters, especially for detecting warfare agents, has not been fully investigated yet. To fill this gap, the molecular modelling of novel inorganic semiconductor nanocluster Ga12As12 as a sensor for phosgene gas (highly toxic for living things and the environment) is accomplished employing benchmark DFT and TD-DFT investigations. Computational tools have been applied to explore different adsorption sites and the potential sensing capability of the Ga12As12 nanoclusters. The calculated adsorption energy (-21.34 ± 2.7 kcal mol-1) for ten selected complexes, namely, Pgn-Cl@4m-ring (MS1), Pgn-Cl@6m-ring (MS2), Pgn-Cl@XY66 (MS3), Pgn-O@4m-ring (MS4), Pgn-O@XY66 (MS5), Pgn-O@XY64 (MS6), Pgn-O@Y (MS7), Pgn-planar@Y (MS8), Pgn-planar@X (MS9), and Pgn-planar@4m-ring (MS10), manifest the remarkable and excessive adsorption response of the studied nanoclusters. The explored molecular electronic properties, such as interaction distance (3.05 ± 0.5 Å), energy gap (∼2.17 eV), softness (∼0.46 eV), hardness (1.10 ± 0.01 eV), electrophilicity index (10.27 ± 0.45 eV), electrical conductivity (∼1.98 × 109), and recovery time (∼3 × 10-12 s-1) values, ascertain the elevated reactivity and an imperishable sensitivity of the Ga12As12 nanocluster, particularly for its complex MS8. QTAIM analysis exhibits the presence of a strong electrostatic bond (positive ∇2ρ(r) values), electron delocalization (ELF < 0.5), and a strong chemical bond (because of high all-electron density values). In addition, NBO analysis explores the lone pair electron delocalization of phosgene to the nanocluster stabilized by intermolecular charge transfer (ICT) and different kinds of non-covalent interactions. Also, the green region existence expressed by NCI analysis (between the nanocluster and adsorbate) stipulate the energetic and dominant interactions. Furthermore, the UV-Vis, thermodynamic analysis, and density of state (DOS) demonstrate the maximum absorbance (562.11 nm) and least excitation energy (2.21 eV) by the complex MS8, the spontaneity of the interaction process, and the significant changes in HOMO and LUMO energies, respectively. Thus, the Ga12As12 nanocluster has proven to be a promising influential sensing material to monitor phosgene gas in the real world, and this study will emphasize the informative knowledge for experimental researchers to use Ga12As12 as a sensor for the warfare agent (phosgene).

Relationship between the Molecular Geometry and the Radiative Efficiency in Naphthyl-Based Bis-Ortho-Carboranyl Luminophores

The efficiency of intramolecular charge transfer (ICT)-based emission on π-aromatic-group-appended closo-ortho-carboranyl luminophores is known to be affected by structural fluctuations and molecular geometry, but investigation of this relationship has been in progress to date. In this study, four naphthyl-based bis-o-carboranyl compounds, in which hydrogen (15CH and 26CH) or trimethysilyl groups (15CS and 26CS) were appended at the o-carborane cage, were synthesized and fully characterized. All the compounds barely displayed an emissive trace in solution at 298 K; however, 15CH and 26CH distinctly exhibited a dual emissive pattern in rigid states (in solution at 77 K and in films), attributed to locally excited (LE) and ICT-based emission, while 15CS and 26CS showed strong ICT-based greenish emission. Intriguingly, the molecular structures of the four compounds, analyzed by single X-ray crystallography, showed that the C-C bond axis of the o-carborane cage in the trimethysilyl group-appended compounds 15CS and 26CS were more orthogonal to the plane of the appended naphthyl group than those in 15CH and 26CH. These features indicate that 15CS and 26CS present an efficient ICT transition based on strong exo-π-interaction, resulting in a higher quantum efficiency (Φ_em) for ICT-based radiative decay than those of 15CH and 26CH. Moreover, the 26CS structure revealed most orthogonal geometry, resulting in the highest Φ_em and lowest k_nr values for the ICT-based emission. Consequently, all the findings verified that efficient ICT-based radiative decay of aromatic group-appended o-carboranyl luminophores could be achieved by the formation of a specific geometry between the o-carborane cage and the aromatic plane.

Antibacterial Potential of 2-(-(2-Hydroxyphenyl)-methylidene)-amino)nicotinic Acid: Experimental, DFT Studies, and Molecular Docking Approach

The problems associated with antibacterial drug discovery have kept the model of antibacterial drug to an extraordinary low level. Humans carry millions of bacteria; some species of bacteria can cause infectious disease, while some are pathogenic. Infectious bacteria which can reproduce quickly in the body can cause diseases such as tuberculosis, cholera, pneumonia, and typhoid, thus arises an urgent need to develop new drugs. Herein, 2-{[(2-hydroxyphenyl)methylidene]amino}nicotinic acid was synthesized from the condensation of o-phenylenediamine and 5-nitrosalicaldehyde followed by detailed characterization by ultraviolet-visible spectroscopy, vibrational studies FT-IR, nuclear magnetic resonance (¹H-NMR, ¹³C-NMR), and gas chromatography coupled with mass spectroscopy (GC-MS). The complex synthesized was screened against selected microbes in order to establish their potential antimicrobial activity using selected known drugs as reference. From the results obtained, the Schiff base exhibited antimicrobial activity against all the tested microorganisms except Candida albicans isolate, which exhibited zero diameter zone of inhibition. The theoretical investigations of the synthesized compounds were computed using density functional theory (DFT) at the B3LYP/6-311 +  + G(d, p) level of theory and in silico molecular docking simulation. By comparing binding affinity of the studied compound and the standard drug (ampicillin), the studied compound docked against bacterial protein showed a high binding affinity for E. coli 6.6 kcal/mol and makes it effective as an antibacterial agent for E. coli.

Theoretical Studies on the Structure and Intramolecular Interactions of Fagopyrins-Natural Photosensitizers of Fagopyrum

Simple Summary

The study determines the spatial structure and intramolecular interactions of fagopyrins—natural photosensitizers of Fagopyrum species. In silico calculations show many fagopyrin conformers characterized by the formation of strong intramolecular interactions.

Abstract

Compounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial and electronic structure and many intramolecular interactions. The nature of the interactions varies in different parts of the molecule. The aim of this study is to determine the structure and intramolecular interactions of fagopyrin molecules. For this purpose, in silico calculations were used to perform geometry optimization in the gas phase. QTAIM and NCI analysis suggest the formation of the possible conformers in the fagopyrin molecules. The presence of a strong OHO hydrogen bond was shown in the anthrone moiety of fagopyrin. The minimum energy difference for selected conformers of fagopyrins was 1.1 kcal∙mol⁻¹, which suggested that the fagopyrin structure may exist in a different conformation in plant material. Similar interactions were observed in previously studied structures of hypericin and sennidin; however, only fagopyrin showed the possibility of brake the strong OHO hydrogen bond in favor of forming a new OHN hydrogen bond.

Synthesis, characterization, and theoretical investigation of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)asmino-4-(2,4-dichlorophenyl)thiazol-5-yl-diazenyl)phenyl as potential SARS-CoV-2 agent

The synthesis of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)amino-4-(2,4 dichlorophenyl)thiazol-5-yl-diazenyl)phenyl is reported in this work with a detailed structural and molecular docking study on two SARS-COV-2 proteins: 3TNT and 6LU7. The studied compound has been synthesized by the condensation of cyanuric chloride with aniline and characterized with various spectroscopic techniques. The experimentally obtained spectroscopic data has been compared with theoretical calculated results achieved using high-level density functional theory (DFT) method. Stability, nature of bonding, and reactivity of the studied compound was evaluated at DFT/B3LYP/6-31 + (d) level of theory. Hyper-conjugative interaction persisting within the molecules which accounts for the bio-activity of the compound was evaluated from natural bond orbital (NBO) analysis. Adsorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties of the experimentally synthesized compound was studied to evaluate the pharmacological as well as in silico molecular docking against SARS-CoV-2 receptors. The molecular docking result revealed that the investigated compound exhibited binding affinity of −9.3 and −8.8 for protein 3TNT and 6LU7 respectively. In conclusion, protein 3TNT with the best binding affinity for the ligand is the most suitable for treatment of SARS-CoV-2.

DFT, ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6,6'-Diamino-1,1',3,3'-tetramethyl-5,5'-(4-chlorobenzylidene)bis[pyrimidine-2,4(1H,3H)-dione]

Heterocyclic compounds, including pyrimidine derivatives, exhibit a broad variety of biological and pharmacological activities. In this paper, a previously synthesized novel pyrimidine molecule is proposed, and its pharmaceutical properties are investigated. Computational techniques such as the density functional theory, ADMET evaluation, and molecular docking were applied to elucidate the chemical nature, drug likeness and antibacterial function of molecule. The viewpoint of quantum chemical computations revealed that the molecule was relatively stable and has a high electrophilic nature. The contour maps of HOMO-LUMO and molecular electrostatic potential were analyzed to illustrate the charge density distributions that could be associated with the biological activity. Natural bond orbital (NBO) analysis revealed details about the interaction between donor and acceptor within the bond. Drug likeness and ADMET analysis showed that the molecule possesses the agents of safety and the effective combination therapy as pharmaceutical drug. The antimicrobial activity was investigated using molecular docking. The investigated molecule demonstrated a high affinity for binding within the active sites of antibacterial and antimalarial proteins. The high affinity of the antibacterial protein was proved by its low binding energy (-7.97 kcal/mol) and a low inhibition constant value (1.43 µM). The formation of four conventional hydrogen bonds in ligand-protein interactions confirmed the high stability of the resulting complexes. When compared to known standard drugs, the studied molecule displayed a remarkable antimalarial activity, as indicated by higher binding affinity (B.E. -5.86 kcal/mol & Ki = 50.23 M). The pre-selected molecule could be presented as a promising drug candidate for the development of novel antimicrobial agents.

Understanding the aqueous chemistry of quinoline and the diazanaphthalenes: insight from DFT study

The inter-fragment interactions at various binding sites and the overall cluster stability of quinolone (QNOL), cinnoline (CNOL), quinazoline (QNAZ), and quinoxaline (QNOX) complexes with H2O were studied using the density functional theory (DFT) approach. The adsorption and H-bond binding energies, and the energy decomposition mechanism was considered to determine the relative stabilization status of the studied clusters. Scanning tunneling microscopy (STM), natural bonding orbitals (NBO) and charge decomposition were studied to expose the electronic distribution and interaction between fragments. The feasibility of formations of the various complexes were also studied by considering their thermodynamic properties. Results from adsorption studies confirmed the actual adsorption of H2O molecules on the various binding sites studied, with QNOX clusters exhibiting the best adsorptions. Charge decomposition analysis (CDA) revealed significant charge transfer from substrate to H2O fragment in most complexes, except in QNOL, CNOL and QNAZ clusters with H2O at binding position 4, where much charges are back-donated to substrate. The O---H inter-fragment bonds was discovered to be stronger than counterpart N---H bonds in the complexes, whilst polarity indices confirmed N---H as more polar covalent than O---H bonds. Thermodynamic considerations revealed that the formation process of all studied complexes are endothermic (+ve ΔH f ) and non-spontaneous (+ve ΔG f ).

Investigation on electronic structure, vibrational spectra, NBO analysis, and molecular docking studies of aflatoxins and selected emerging mycotoxins against wild-type androgen receptor

The geometry, frontier molecular orbitals (FMOs), vibrational, NBO analysis, and molecular docking simulations of aflatoxins (B1, B2, M1, M2, G1, G2), zearalenone (ZEA) emodin (EMO), alternariol (AOH), alternariol monoethyl ether (AMME), and tenuazonic acid (TeA) mycotoxins have been extensively theoretically studied and discussed based on quantum density functional theory calculations using Gaussian 16 software package. The theoretical computation for the geometry optimization, NBOs, and the molecular docking interaction was conducted using Density Functional Theory with B3LYP/6-31+G(d,p), NBO program, and AutoDock Vina tools respectively. Charge delocalization patterns and second-order perturbation energies of the most interacting natural bond orbitals (NBOs) of these mycotoxins have also been computed and predicted. Interestingly, among the mycotoxins investigated, aflatoxin G1 is seen to give the strongest stabilization energy while Zearalenone shows the highest tendency to accept electron(s) and emodin, an emerging mycotoxin gave the best binding pose within the androgen receptor pocket with a mean binding affinity of -7.40 kcal/mol.

Synthesis, characterization, DFT, and TD-DFT studies of (E)-5-((4,6-dichloro-1,3,5-triazin-2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2,7-diylbis(hydrogen sulfite)

In this study, (E)-5-((4,6-dichloro-1,3,5-triazin-2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2,7-diylbis(hydrogen sulfite), a cyanurated H-acid (CHA) azo dye, was synthesized and characterized using FT-IR spectrophotometer and GC-MS spectroscopy. A density functional theory (DFT) based B3LYP and CAM-B3LYP method with 6–311 + G (d,p) basis set analysis was computed for HOMO-LUMO, natural bonding orbitals (NBO), UV-Vis absorptions and excitation interactions, in order to understand its molecular orbital excitation properties. A low Energy gap (Eg) of 2.947 eV was obtained from the molecular orbital analysis, which showed that HOMO to LUMO transition is highly feasible; hence CHA is adequate for diverse electronic and optic applications. Studies of the first five excitations (S0 → S1/S2/S3/S4/S5) of CHA revealed that S0 → S1 and S0 → S3 are π → π* type local excitations distributed around the –N=N– group; S0 → S2, a Rydberg type local excitation; S0 → S4, a highly localized π → π* excitation; while S0 → S5 is an n → π* charge transfer from a benzene ring to –N=N– group. From NBO analysis, we obtained the various donor–acceptor orbital interactions contributing to the stabilization of the studied compound. Most significantly, some strong hyper-conjugations (n → n*) within fragments, and non-bondingand anti-bonding intermolecular (n → n*/π* and π → n*/π*) interactions were observed to contribute appreciable energies. This study is valuable for understanding the molecular properties of the azo dyes compounds and for synthesizing new ones in the future.

Theoretical investigation of the stability, reactivity, and the interaction of methyl-substituted peridinium-based ionic liquids

This research work focuses on the reactivity, stability, and electronic interaction of pyridinium hydrogen nitrate (PHN)-based ionic liquids and the influence of methyl substituent on this class of ionic liquids: Ortho- (O-MPHN), meta- (M-MPHN), and para- (P-MPHN) substitution. Natural bond orbital (NBO) calculations were performed at the density functional theory (DFT) with Becke’s Lee Yang and Parr functional (B3LYP) methods and DFT/B3LYP/6-311++G(d,p) as basis set using GAUSSIAN 09W and GAUSSVIEW 6.0 software and the most important interaction between donor (Filled Lewis-type NBO’s) and the acceptor (vacant non-Lewis NBOs) were observed. From our natural bond orbital (NBO) result, it could be deduced that the higher the stabilization energy value, the greater the interaction between the donor and acceptor NBOs. The stability of the studied compounds is said to follow the order from O-MPHN > PHN > P-MPHN > M-MPHN based on the hyperconjugative interaction (stabilization energy) of the most significant interaction. The result of the highest occupied molecular orbital (HOMO), shows that PHN has the highest HOMO while the substituted derivatives have similar HOMO values between −7.70 and −7.98 eV thus PHN complex is the best electron donor while the substituted derivatives act as electron acceptors due to the presence of methyl group substituent which is observed to be electron deficient as a result of its withdrawal effect from the aromatic ring. Furthermore, the electron density, real space functions such as energy density and Laplacian of electron density at bond critical point (BCP) of the hydrogen bond interaction of the studied compounds were analyzed using Multifunctional Wavefunction analyzer software version 3.7 and it was observed that the hydrogen at position 6 and oxygen at position 11 (H6–O11) of M-methyl pyridinium nitrate with bond distance of 4.59 (Å) gave binding energy with the strongest electrostatic interaction between the cation and anion of the compounds under investigation. We also observed from our results that, substitution at the ortho position enhances the stability and strengthen the extent of charge transfer. This therefore implies that substitution at ortho position is more favorable for inter- and intramolecular interactions resulting to stabilization of the studied molecules.