English العربية کوردی
01004015

د. Haydar Abdulhakim Mohammad-Salim

Assistant Professor
College of Science / Department of Chemistry
07504806052
hayder.salim@uoz.edu.krd
ژمارەی بڵاوکراوەکان: 88
0
خەڵاتەکان
88
توێژینەوە زانستییەکان
2
تێز و نامەکان
0
خولەکان

0
کتێبەکان
6
کۆنفرانسە زانستییەکان
0
پێشکەشکردنەکان
2
وۆرکشۆپەکان
2024
PostDoc in Molecular Topology and Drug Design

University of Valencia
University of Valencia

2020
Doctor of Philosophy

Department of Chemistry
University of Zakho

2012
Master

Chemical Engineering
Swansea University

2009
Bachelor

Department of Chemistry
University of Duhok

Google scholar
Researchgate
Linkedin
Academia
Assistant Professor

بەروار: 2020-12-16

Lecturer

بەروار: 2016-09-18

Assistant Lecturer

بەروار: 2013-05-28

2026

Synthesis and multiscale computational analysis of 6-nitrobenzoxazole-2-thione: electronic structure, intermolecular interactions, and predicted protease inhibition
New Journal of Chemistry (ژمارەی وەرز (Issue) : 5) (بەرگ (Volume) : 50)
Nitro-substituted benzoxazole-2-thione derivatives constitute an underexplored class of heteroaromatic systems with promising pharmacological potential. In this study, 6-nitrobenzoxazole-2-thione was successfully synthesized via regioselective nitration of benzoxazole-2-thione and fully characterized by IR, 1H and 13C NMR spectroscopy, high-resolution mass spectrometry, and single-crystal X-ray diffraction, confirming its molecular structure and thione tautomeric form. Density functional theory (DFT) calculations performed at the M06-2X-D3/6-311++G(d,p) level reveal a kinetically stable and moderately hard electronic system, characterized by a HOMO–LUMO gap of 6.625 eV and a pronounced electrophilic character. Electrostatic potential mapping highlights highly negative regions localized on the nitro oxygen atoms and the thione sulfur, identifying key sites for hydrogen-bond acceptance and intermolecular recognition. Hirshfeld surface analysis demonstrates that the crystal packing is predominantly governed by dispersive H⋯H interactions, supplemented by directional heteroatom-centered hydrogen bonds. Ligand-based activity prediction (PASS) indicates strong inhibition potential toward aspartic proteases, including saccharopepsin, chymosin, and acrocylindropepsin (Pa ≈ 0.807), which is further supported by molecular docking and molecular dynamics simulations revealing stable binding modes within the enzyme active site. However, ADMET profiling, while confirming favorable drug-like physicochemical properties, highlights significant metabolic and toxicity risks, particularly associated with CYP inhibition and predicted hepatotoxicity, suggesting the need for structural optimization. Overall, this integrative experimental and multiscale computational study establishes 6-nitrobenzoxazole-2-thione as a promising electrophilic heteroaromatic scaffold and provides a comprehensive structure–property–activity relationship framework for the rational design of benzoxazole-based protease inhibitors.
2026-05
Mechanistic insights into furan-based Diels–Alder cycloadditions: an ELF, BET, NCI, AIM, and MEDT study
Theoretical Chemistry Accounts (ژمارەی وەرز (Issue) : 5) (بەرگ (Volume) : 145)
Diels–Alder (DA) cycloadditions are potent atom-economical transformations for the formation of six-membered cycloadducts with excellent regio- and stereoselectivity. The DA 4 + 2 cycloaddition between furan-2-ylmethanol and N-phenylmaleimides with para-substituents (X = H, F, Cl, Br) is studied using MEDT and density functional theory calculations at the M06‑2X(D3)/6‑311G(d,p) level. The polarity of the studied cycloaddition reaction was determined using conceptual DFT (CDFT) indices, natural population analysis (NPA), and global electron density-transfer (GEDT) values to quantify the electronic properties of the reagents and track the expected flow of electron density. In all substitution patterns, exo path is projected to be more favorable than endo path. The transition states’ polarity is corroborated by high GEDT values (≈ 0.26–0.28 e), showing electron density transfer from the furan-derived diene to the maleimide framework. Electron localization function (ELF) topological analysis for reactants and transition states was combined with bonding evolution theory (BET) along intrinsic reaction coordinates (IRC) to better understand chemical bond formation and how substituents affect it. These analyses suggest a two-stage, one-step (asynchronous) cycloaddition in which the new C–C bond is formed earlier at the transition state than the second bond involving the heteroatom-containing fragment, indicating a polar, nonsynchronous bonding reorganization rather than a perfectly coordinated event. Additional QTAIM and NCI descriptions show developing interactions at the forming bond critical points and weak stabilizing noncovalent contacts that favor exo transition structures. Electron-withdrawing substituents enhance electrophilicity of dienophile and subtly modulate energetics and electron density redistribution along the exo path, explaining the impact of phenyl-ring halogen substitution.
2026-05
Experimental and computational investigation of ortho/para azobenzaldehyde isomers: synthesis, DFT, molecular docking, and molecular dynamics insights
Structural Chemistry (ژمارەی وەرز (Issue) : 4) (بەرگ (Volume) : 38)
A diazotization–coupling route was used to synthesize the para (4) and ortho (5) azobenzaldehyde isomers, which were fully characterized by FT-IR, ¹H/¹³C NMR and MS techniques. Global reactivity descriptors were computed at the M06-2X-D3/6-311G(d, p) level. The para form has a much stronger NBO stabilization energy (≈ 4771 vs. 3187 kcal·mol⁻¹), thus it is more delocalized and polarizable, while the ortho remains a slightly harder and more electronegative. Molecular docking on the target 2IOK, validated by redocking of the co–crystallized ligand (RMSD = 1.553 Å), reveals nearly identical binding affinities for both isomers (para − 8.45; ortho − 8.44 kcal·mol− 1) and a common hydrophobic anchoring pattern involving PHE, LEU and MET residues, augmented by polar contacts with HIS524 and ARG394; however, the para isomer establishes a somewhat richer polar interaction network. The docked …
2026-04
Unveiling the reaction mechanism and the regioselectivity of Diels–Alder cycloadditions between 2-methoxy-3-thiophenylbutadiene and methyl vinyl ketone using topological tools
RSC advances (ژمارەی وەرز (Issue) : 19) (بەرگ (Volume) : 16)
The [4 + 2] Diels–Alder cycloaddition reaction between 2-methoxy-3-thiophenylbutadiene 1 and methyl vinyl ketone 2 has been studied at the density functional theory level using a panoply of tools to unravel the regioselectivity and the reaction mechanisms. From the analysis of the CDFT reactivity indices, 2 behaves as an electrophile, while 1 behaves as a nucleophile. This cycloaddition is characterized by a non-polar character as evaluated by a low value of the electrophilicity difference between the reactants as well as a low value of the global electron density transfer at the transition state. Futher, the bonding evolution theory shows that this reaction takes place via a one-step asynchronous mechanism. QTAIM descriptors also highlight the asynchronicity, which confirms the absence of the formation of a new covalent bond. Generally, the ortho/endo pathway is both thermodynamically and kinetically favored over …
2026-03
Mechanistic and Regioselective insights into thermal and ruthenium (II)-catalyzed (3 + 2) cycloadditions of nitrile N-oxide with internal thioalkyne: a combined on Isoxazole derivatives, molecular docking, ADMET approach, MD and PASS simulations from the MEDT perspective
Computational and Theoretical Chemistry (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 1256)
This study investigates uncatalyzed and ruthenium (II)-catalyzed (3 + 2) cycloaddition (32CA) reactions between nitrile N-oxide and internal thioalkyne using the M06-2×-D3 level of theory.The def2-TZVPD basis set was employed for Ru atoms, and 6-311G(d,p) for all others. Uncatalyzed pathways toward 1,4- and 1,5-isoxazole regioisomers exhibited comparable Gibbs free energies (−65.7 and − 60.3 kcal·mol−1), indicating minimal regioselectivity, consistent with experimental observations. Ru(II) catalysis significantly enhanced regioselectivity by modulating electronic structures and bonding evolution. ELF and CDFT analyses confirmed the zwitterionic character of nitrile N-oxide and electron density transfer from thioalkynes. GEDT values revealed low-polarity thermal pathways versus more polar Ru-catalyzed ones.BET supported a stepwise mechanism in uncatalyzed reactions and catalyst-dependent modulation in Ru(II)-mediated systems.Molecular docking against MCF-7 protein(PDB: 3ERT)indicated moderate binding affinities (−9.3 and − 9.7 kcal·mol−1) compared to the reference ligand (−13.1 kcal·mol−1). ADMET, toxicity,MD simulations, and PASS predictions suggest favorable pharmacokinetic and anticancer potential for both regioisomers,underscoring their mechanistic and biological relevance.
2026-02
Phytochemical and antibacterial studies of the ethanolic stem barks extract of Anthocleista vogelii planch, and the in silico study of its secondary metabolites on two bacteria strains Staphylococcus aureus and Salmonella typhi
Zeitschrift für Naturforschung C A Journal of Biosciences (ژمارەی وەرز (Issue) : 3) (بەرگ (Volume) : 81)
This study investigates the phytochemical composition, antibacterial efficacy, and molecular interactions of Anthocleista vogelii stem barks extracts. Phytochemical screening revealed the presence of flavonoids, alkaloids, triterpenes, phenols, saponins, and other bioactive compounds in 95 % ethanol and hydro-ethanol extracts, while coumarins, steroids, and anthraquinones were absent in aqueous extracts. The 95 % ethanol extract demonstrated significant antibacterial activity against Esherichia coli (MIC: 64 μg/mL) and Klebsiella pneumoniae (MIC: 8 μg/mL), with moderate effects against Staphylococcus aureus, A. baumannii, and Salmonella Spp. (MIC: 512 μg/mL). Bactericidal activity (MBC/MIC ≤ 4) paralleled ciprofloxacin, particularly against Gram-positive pathogens. LC-MS analysis identified nine bioactive flavone derivatives, including fabiatrin, kaempferitrin, quercitrin, and naringin. Molecular docking revealed these compounds exhibited superior binding affinities (−6.6 to −11.7 kcal mol−1) to S. aureus and Salmonella typhi targets compared to ciprofloxacin (−3.6 to −5.4 kcal mol−1), forming hydrogen bonds and π-interactions critical for inhibition. ADMET predictions indicated poor gastrointestinal absorption and AMES toxicity risks but favorable plasma protein binding and cardiac safety. Frontier Molecular Orbital (FMO) analysis highlighted quercetin’s high reactivity (ΔEgap: 3.70 eV) and naringin’s stability. These findings position A. vogelii as a rich source of antimicrobial phytochemicals, though further optimization is needed to address pharmacokinetic limitations.
2026-02
Mechanistic insights into (3+ 2) cycloaddition of glutaraldehyde-N-Aryl nitrone with cinnamaldehyde: Electron density, docking, and molecular dynamics analysis
Structural Chemistry (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 37)
This study investigates the [3+ 2] cycloaddition (32CA) reaction between Glutaraldehyde-N-aryl nitrone (GN-1) and Cinnamaldehyde (CA-2) to elucidate its mechanistic pathway and biological relevance. Understanding this reaction is important because it leads to the synthesis of pharmacologically significant isoxazolidine derivatives, compounds with therapeutic potential. Using Density Functional Theory (DFT) within the framework of Molecular Electron Density Theory (MEDT), we explored the potential energy surface (PES) and identified four stereoisomeric routes. The ortho-endo pathway was found to be both thermodynamically (ΔG=− 8.92 kcal. mol⁻ ¹) and kinetically the most favorable. Global Electron Density Transfer (GEDT) analysis indicated a forward electron density flux (FEDF) of 0.0594 e, confirming a polar mechanism. Electron Localization Function (ELF) and Bonding Evolution Theory (BET) analyses …
2026-01

2025

Convenient synthesis, spectroscopy characterization, biological evaluation, and computational studies of Azo-chalcone for DNA detection
Journal of Molecular Structure (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 1342)
This study reports the synthesis and characterizing of a novel azo-chalcone incorporating a dimethylamino-diazenylphenyl fragment, designed as a safer organic dye for DNA staining. Spectroscopic methods (IR, ¹H/¹³C NMR) confirmed the structure, while density functional theory (DFT) revealed its electronic properties, demonstrating comparable reactivity in gas and ethanol phases with enhanced electrophilicity in solution. Molecular docking identified minor groove binding to A-T-rich DNA regions (docking score: -8.212 kcal/mol), supported by hydrogen bonds and van der Waals interactions. The compound adhered to Lipinski’s rule of five and exhibited favorable ADMET profiles, though risks of CYP inhibition and hepatotoxicity were noted. Hirshfeld surface analysis highlighted weak non-covalent interactions, while MEP mapping identified nucleophilic sites at carbonyl oxygen. This work advances chalcone …
2025-10
MEDT insights into the mechanism and selectivity of the (3 + 2) cycloaddition of (Z)-N-methyl-C-(2-furyl)-nitrone with but-2-ynedioic acid and the bioactivity of the reaction products
RSC Advances (ژمارەی وەرز (Issue) : 15) (بەرگ (Volume) : 39)
In this contribution, Molecular Electron Density Theory (MEDT) is employed to investigate the (3 + 2) cycloaddition reaction between (Z)-N-methyl-C-(2-furyl)-nitrone 1 and but-2-ynedioic acid 2. DFT calculations at the M06-2X-D3/6-311+G(d,p) level of theory under solvent-free conditions at room temperature show that this reaction proceeds viaCA3-Z diastereoselectivity, with the formation of the CA3-Z cycloadduct being both thermodynamically and kinetically more favoured than the CA4-Z one. Reactivity parameters obtained from CDFT calculations reveal that compound 1 predominantly behaves as a nucleophile with moderate electrophilic features, in contrast to compound 2, which demonstrates strong electrophilicity and limited nucleophilic ability. This disparity in electronic properties suggests a polar mechanism for the investigated 32CA reaction. Then, bonding evolution theory shows that this cycloaddition proceeds via a one-step asynchronous process. On the other hand, both CA3-Z and CA4-Z cycloadducts demonstrate promising characteristics as lead compounds for drug development. Molecular docking studies indicate moderate affinity toward the 7BV2 protease, while their physicochemical properties and compliance with major drug-likeness rules support their potential as orally bioavailable agents. Furthermore, PASS predictions suggest a wide range of biological activities, notably in inflammation, neuroprotection, and anticancer applications. These findings, in line with experimental cytotoxicity data, highlight the therapeutic potential of these isoxazolidine derivatives and warrant further experimental validation.
2025-09
Molecular docking and computational assessment of spectroscopic analysis of ethyl 3-(4-chloro-2-methylphenylamino)-3-phenylacrylate as a potential antibacterial agent
New Journal of Chemistry (ژمارەی وەرز (Issue) : 34) (بەرگ (Volume) : 49)
A novel enamino ester, ethyl 3-(4-chloro-2-methylphenylamino)-3-phenylacrylate 3, was synthesized and structurally characterized. Density functional theory (DFT) calculations at the B3LYP-D3/6-311++G(d,p) level were used to investigate its molecular geometry and predict NMR chemical shifts, which showed good agreement with experimental data. Electronic properties, including the HOMO–LUMO gap, Fukui functions, and molecular electrostatic potential (MEP) surface, indicated both chemical stability and potential reactive sites. Molecular docking analysis revealed promising antibacterial activity, with compound 3 showing favorable binding to Bacillus subtilis laccase, E. coli DNA gyrase B, and key residues in Staphylococcus aureus. ADME-Tox predictions confirmed acceptable pharmacokinetic properties and low toxicity, notably with no significant hERG inhibition or neurotoxicity risk. Overall, compound 3 emerges as a stable and bioactive molecule with potential for further antibacterial drug development.
2025-08
Mechanistic insights into the (3+ 2) cycloaddition of azomethine ylide with dimethyl acetylenedicarboxylate via bond evolution theory
RSC advances (ژمارەی وەرز (Issue) : 36) (بەرگ (Volume) : 15)
The mechanistic pathway of the (3 + 2) cycloaddition (32CA) between azomethine ylide 1 and dimethyl acetylenedicarboxylate 2, affording 4-isoxazoline derivatives, was elucidated via Density Functional Theory (DFT) calculations employing the B3LYP-D3 functional and the 6-311++G(d,p) basis set in 1,4-dioxane. Reactivity insights derived from Conceptual DFT (CDFT) demonstrated that compound 1 behaves as an ambiphilic species with significant nucleophilic and electrophilic tendencies, whereas compound 2 functions predominantly as an electrophile. These electronic features reveal a marked polarity in the cycloaddition and align with a forward electron density flux (FEDF) governing the reaction process. Natural Population Analysis (NPA) and Parr functions identified the C3 carbon of 1 as the most nucleophilic center and the C4/C5 carbons of 2 as the most electrophilic, suggesting initial C3–C4 bond …
2025-08
Mechanistic Study of N‐t‐Butyl Nitrone and Nitroethene (3+ 2) Cycloaddition: A Combined DFT, Docking, and ADMET Approach
Journal of Heterocyclic Chemistry (ژمارەی وەرز (Issue) : 10) (بەرگ (Volume) : 62)
In this study, the (3 + 2) cycloaddition 32CA reaction between N‐t‐butyl nitrone 1 and nitroethene 2 was comprehensively investigated using density functional theory (DFT), electron localization function (ELF), atoms‐in‐molecules (AIM) analysis, and ADMET profiling. The reaction paths were examined in terms of regio‐ and stereoisomeric outcomes, with four possible cycloadducts being characterized. DFT‐based reactivity indices indicated a strong polar nature of the reaction, with the global electrophilicity index (ω) and nucleophilicity index (N) suggesting that nitroethene acts as a strong electrophile and the nitrone as a strong nucleophile. A significant global electron density transfer (GEDT) from the nitrone 1 to nitroethene 2 was observed at the transition states (0.19–0.23 e), confirming a polar character and forward electron density flux (FEDF). Topological analysis of ELF along the reaction coordinate …
2025-08
Claisen–Schmidt synthesis of azo-chalcone catalyzed by a zinc-based metal–organic framework: structural characterization, density functional theory calculations, and molecular docking studies
Reaction Kinetics, Mechanisms and Catalysis (ژمارەی وەرز (Issue) : 6) (بەرگ (Volume) : 138)
A novel zinc-based metal–organic framework was successfully employed as a catalyst in the Claisen–Schmidt condensation reaction for the synthesis of azo-chalcone. The catalyst demonstrated excellent recyclability and maintained high activity after the reaction without loss of effectiveness. The synthetic protocol allows for simple product isolation, easy workup, and efficient purification, supporting potential scale-up for industrial applications. Quantum chemical calculations provided insights into the electronic and structural properties of the synthesized azo-chalcone. Molecular docking studies revealed strong binding affinity of the chalcone to Escherichia coli DNA gyrase, with a docking score of − 10.794 kcal/mol. Key interactions involved hydrogen bonding and van der Waals forces, particularly with the amino acid Asn46, which is critical in ATP hydrolysis inhibition. The compound also displayed favorable drug …
2025-08
Boronate ester-based covalent organic framework as a porous biosensor for anticancer and anti-inflammatory agents: A DFT study on curcumin and crizotinib
Computational and Theoretical Chemistry (ژمارەی وەرز (Issue) : 11) (بەرگ (Volume) : 1252)
This study explores the potential of boronate ester-based COF-1 as a biosensor for anticancer and anti-inflammatory drugs, specifically curcumin and crizotinib, using Density Functional Theory (DFT). Interaction energies, NCI, QTAIM, EDA, and FMO analyses indicate that van der Waals forces mainly govern adsorption. Crizotinib exhibits stronger binding, greater charge transfer, reduced HOMO-LUMO gap, and higher dipole moment, enhancing sensor selectivity and conductivity. Recovery time analysis suggests faster desorption of crizotinib, supporting its suitability for real-time sensing. Overall, COF-1 shows promise as an effective sensor, especially for crizotinib, with applications in drug monitoring and biomedical diagnostics.
2025-07
A Molecular Electron Density Theory Study for the Synthesis of Spirocyclic and Tricyclic Isoxazolines and Their Molecular Docking Evaluation for Antituberculosis Activity
Journal of Physical Organic Chemistry (ژمارەی وەرز (Issue) : 8) (بەرگ (Volume) : 38)
The [3 + 2] cycloaddition (32CA) reactions of aryl and heteroaryl nitrile oxides with (S)‐(−)‐β‐pinene and (R)‐(+)‐α‐pinene have been theoretically studied from the Molecular Electron Density Theory (MEDT) perspective and a molecular docking evaluation for the antituberculosis activity of the isoxazoline products. The studied 32CA reactions show activation Gibbs free energies between 23.8 and 31.6 kcal·mol−1, consistent with their zwitterionic character and exclusive regioselectivity, in complete agreement with the experiments. Two‐stage one‐step mechanism with a very low polar character is predicted. The molecular mechanism has been established from the Bonding Evolution Theory (BET) analysis along the reaction path, showing early transition state structures, with weak non‐covalent interactions indicated from the quantum theory of atom‐in‐molecules (QTAIM) analysis. The isoxazoline products for …
2025-07
Microwave-Assisted Synthesis of Azo-Chalcone Using Porous MOF Catalysts: Insights from DFT and Molecular Docking
Catalysis Letters (ژمارەی وەرز (Issue) : 8) (بەرگ (Volume) : 155)
Metal-organic frameworks (MOFs)-derived heterogeneous catalysis has gained significant attention for their catalytic efficacy and unique structural features, making them valuable in various organic syntheses by enhancing reaction efficiency, selectivity, and sustainability. MOFs are highly effective catalysts in organic synthesis due to their catalytically active sites, significant surface areas, tunable pore structures, and a wide range of chemical characteristics that enhance selectivity and accelerate reactions. This study introduces the application of a novel MOF (called UoZ-2) as a heterogeneous catalyst for synthesizing a novel azo-chalcone product through the Claisen-Schmidt condensation process. The UoZ-2 acid catalyst is esteemed for its many benefits, such as operating under mild conditions, achieving rapid reaction rates, facilitating straightforward recovery and isolation without diminishing catalytic efficiency …
2025-07
Decoding the [3+ 2] cycloaddition of a furan–imine oxide with styrene: mechanism, selectivity and bioactivity
Organic & Biomolecular Chemistry (ژمارەی وەرز (Issue) : 28) (بەرگ (Volume) : 23)
In this investigation, molecular electron density theory (MEDT) is used to study the [3 + 2] cycloaddition (32CA) reaction between 1-(furan-2-yl)-N-phenylmethanimine oxide (1) and styrene (2). In fact, density functional theory (DFT) calculations at the M06-2X-D3/6-311G(d,p) level of theory in benzene at room temperature were performed to describe the regio- and stereoselectivity and the mechanism of the 32CA reaction studied. Using the CDFT approach, 1 is a moderate electrophile and a strong nucleophile, while 2 is classified as a moderate electrophile and a moderate nucleophile. As a consequence, the 32CA reaction under study is characterized by a non-polar characteristic. Analysis of thermodynamic data indicates that the meta–endo compound is both thermodynamically and kinetically more favored than the other compounds, which aligns perfectly with the experimental results. BET analysis shows that …
2025-06
Catalytic performance of cobalt-based heteronuclear dual transition metal-doped graphitic carbon nitride systems for ammonia synthesis: Insights from density functional theory
Surfaces and Interfaces (ژمارەی وەرز (Issue) : 15) (بەرگ (Volume) : 71)
In recent years, the global demand for sustainable ammonia synthesis has risen significantly, emphasizing the need for alternatives to the environmentally harmful and inefficient Haber-Bosch process. This study explores the catalytic potential of heteronuclear dual transition metal systems (M1M2@g-C6N6) using density functional theory (DFT). Nine Co-based dual-metal catalysts (CoSc, CoTi, CoV, CoCr, CoMn, CoFe, CoNi, CoCu, and CoZn) were evaluated based on adsorption energy, binding energy, and limiting potential across distal, alternating, and enzymatic pathways. The CoSc@g-C6N6 emerged as the most efficient catalyst, displaying a low limiting potential of 0.53 eV in enzymatic pathway. The CoSc@C6N6 also showed least energy barrier in distal (0.88 eV) and alternating pathways (0.68 eV). The N2 bond elongation has been noticed from 1.11 Å to 1.18 Å in the enzymatic pathway, indicating the effective nitrogen activation. Moreover, CoSc@g-C6N6 demonstrated consistent performance across all pathways, effectively suppressing the hydrogen evolution reaction (HER), being more selective for nitrogen reduction to ammonia. In contrast, rest of candidates with higher energy barriers and less favorable adsorption properties, were excluded. This study highlights the importance of dual-metal catalysts and electronic structure optimization in achieving efficient and selective nitrogen reduction. The findings contribute potentially to the ENRR mechanism and sustainable catalysis (SuCat) research. The results identify CoSc@g-C6N6 as a promising candidate for experimental validation which is a significant step towards sustainable ammonia production.
2025-06
Mechanistic insights into the regio- and stereoselectivity of [3+2] cycloaddition reactions between N-methyl-phenylnitrone and trans-1-chloro-2-nitroethylene within the framework of molecular electron density theory
New Journal of Chemistry (ژمارەی وەرز (Issue) : 26) (بەرگ (Volume) : 49)
The [3+2] cycloaddition (32CA) reaction between N-methyl-phenylnitrone 1 and trans-1-chloro-2-nitroethylene 2 has been studied using molecular electron density theory (MEDT) to analyze the reaction mechanism and the regio- and stereoselectivity. The global reactivity indices show that 2 is classified as a strong electrophile while 1 is a strong nucleophile. Four reaction pathways, including ortho/meta regioselective and endo/exo stereoselective modes, were explored in vacuo and in solution (benzene, ε = 6.0). The study reveals ortho regioselectivity with high endo stereoselectivity, consistent with experimental results. The BET study shows a one-step asynchronous reaction mechanism, where the O–C bond forms before the C–C bond in ortho (endo and exo) pathways and inversely in the meta ones. The ELF analysis of the reaction mechanism involves the depopulation of V(N,C) and V(C,C) basins of 1 and 2 …
2025-05
Computational investigation of the cycloaddition reaction mechanism of 2,4,6-trimethyl-3,5-dichlorobenzonitrile N-oxide with arylacetylenes: insights from density functional theory and molecular docking
Reaction Kinetics, Mechanisms and Catalysis (ژمارەی وەرز (Issue) : 2025) (بەرگ (Volume) : 138)
This study investigates the mechanistic pathways of the [3+2] cycloaddition (32CA) reaction between 2,4,6-trimethyl-3,5-dichlorobenzonitrile N-oxide 1 and arylacetylenes 2 (2a, 2b, 2c, and 2d) using Molecular Electron Density Theory (MEDT). However, Density Functional Theory (DFT) calculations at the B3LYP/6-311++G(d,p) level were employed to analyze the electron density distribution and reaction energetics. Parr functions were employed to identify the most electrophilic and nucleophilic centers, providing insights into regioselectivity and reactivity trends. The Global Electron Density Transfer (GEDT) values confirm the polar nature of the reaction, indicating a forward electron density flux (FEDF) mechanism. Bonding Evolution Theory (BET) was applied along the Intrinsic Reaction Coordinate (IRC) to analyze electronic structure transformations, revealing a non-concerted, asynchronous bond formation …
2025-05
Mechanistic study of the [2+ 2] cycloaddition of ethylene with ketene derivatives via MEDT
Structural Chemistry (ژمارەی وەرز (Issue) : 6) (بەرگ (Volume) : 36)
In this study, the [2 + 2] cycloaddition reaction between ethylene 1 and ketene 2, along with its chalcogen-substituted derivatives 3–5, leading to the formation of four-membered rings, was investigated within the framework of Molecular Electron Density Theory (MEDT) at the B3LYP-D3/6–311 + + G(d,p) level of theory. The dimerization of ethylene exhibits a high activation Gibbs free energy (ΔG≠ = 88.0 kcal mol−1), reflecting the nonpolar nature of this reaction, which follows a one-step asynchronous mechanism. The incorporation of chalcogen atoms into the ethylene framework leads to a moderate reduction in activation energy, following the trend ketene (2, X = O) > thioketene (3, X = S) > selenoketene (4, X = Se) > telluroketene (5, X = Te). This decrease in activation energy is accompanied by an increase in the reaction’s polarity, as evidenced by the electrophilicity difference between the …
2025-05
Deciphering the Mechanism and Stereoselectivity of the [3+ 2] Cycloaddition Between C-(D-Glucoso)-N-Methyl Nitrone and 1H-Pyrrole-2, 5-Dione: A MEDT Investigation
Organic & Biomolecular Chemistry (ژمارەی وەرز (Issue) : 16) (بەرگ (Volume) : 23)
In this study, a molecular electron density theory (MEDT) is used to describe the reaaction mechanism and the experimental stereoselctivity of the [3+2] cycloaddition (32CA) reactions of C-(D-glucoso)-N-methyl nitrone 1 and 1H-pyrrole-2,5-dione 2. From the analysis of the global reactivity indices, 2 behave as electrophiles while 1 as nucleophile. Then, Bonding Evolution Theory (BET) reveals that this 32CA reaction takes place via a one-step asynchronous process with the formation of the C–C bond before the O–C one along of both endo and exo pathways. Further, topological ELF and QTAIM analyses confirmed the asynchronous character of the bond formations along with the polarity of the reaction evaluated by the computed GEDT at the TSs. Generally, the endo pathway is both thermodynamically and kinetically favored than the exo one. Finally, using the Distortion/Interaction-Activation Strain, it is shown that the endo/exo selectivity is mostly driven by the differences of interaction energies.Moreover, molecular docking analyses revealed that the endo product has considerable binding affinity to the 1CIN protease, indicating its potential as a therapeutic inhibitor. Moreover, drug-likeness evaluations verified that the compounds adhere to Lipinski's Rule of Five, signifying advantageous pharmacokinetic characteristics. This extensive work combines theoretical and computational approaches to clarify the intricate processes of 32CA reactions, offering significant insights into their synthetic applications and possible medicinal benefits.
2025-04
Unveiling Intramolecular [3+2] Cycloaddition Reactions Leading to Functionalized Heterocycles in the Light of Molecular Electron Density Theory
ChemPhysChem (ژمارەی وەرز (Issue) : 7) (بەرگ (Volume) : 26)
The kinetically controlled intramolecular [3+2] cycloaddition (IM32CA) reactions are predicted to be cis stereospecific, while the reaction feasibility follow the order NY>NS>NO>AZ. The decreased activation energy of NY could be correlated with its carbenoid character, relative to the zwitterionic one predicted for the other three species. The markedly reduction of the unfavorable activation entropy associated with these intramolecular reactions is responsible for the feasibility of these IM32CA reactions.
2025-04
Unveiling Hydrogen Bonding and Solvent Effects on Directed Nitrile Oxide [3 + 2] Cycloaddition Reactions: Selectivity of 2,2-Dimethylpropane Nitrile Oxide with Cyclopentenylbenzamide: An MEDT Study
ACS Omega (ژمارەی وەرز (Issue) : 10) (بەرگ (Volume) : 15)
The role of hydrogen bond and solvent effects on the regio- and diastereoselectivity of the [3 + 2] cycloaddition reaction (32CA) between 2,2-dimethylpropanenitrile oxide (NO) and N-(cyclopent-2-en-1-yl)benzamide has been theoretically studied at the B3LYP/6-311++G(d,p) level using the molecular electron density theory (MEDT). Solvent effects of dichloromethane (DCM) and benzene were taken into account. The electron localization function (ELF) classifies NO as a three-atom component with a zwitterionic electronic structure, which participates in zwitterionic-type 32CA reactions. The reactions occur through a one-step mechanism and present high activation Gibbs free energies in DCM and in benzene, with a slight difference favoring the reaction in benzene. Along the intrinsic reaction coordinate reaction pathway, the topological analysis of the ELF shows the asynchronous formation of the C–C bond prior to the C–O bond by coupling the two-carbon pseudoradical centers. The low global electron density transfer indicates that these reactions have a nonpolar character, which accounts for their high Gibbs free activation energies. Analysis of the noncovalent interactions associated with the TSs reveals a hydrogen bond in the favored TS, which confirms its participation in the experimental selectivities.
2025-04
Identification of Potential Inhibitors of Plasmodium falciparum L-lactate Dehydrogenase From Selected African Compound Libraries: Virtual Screening, Molecular Mechanics-Generalized Born Surface Area, and Molecular Dynamics Studies
Chemistry & Biodiversity (ژمارەی وەرز (Issue) : 9) (بەرگ (Volume) : 22)
We evaluated 4,512 natural products from natural product library from Central African medicinal plants for drug discovery and South African natural compounds database libraries for the identification of potential Plasmodium falciparum L‐lactate dehydrogenase inhibitors considering the virtual screening process. Extra precision virtual screening enabled the ranking of the top hundred hit molecules based on their docking properties. The selected hits were further shortened based on docking and molecular mechanics‐generalized born surface area parameters in comparison with the reference. As a result, four hits were chosen: Mol1, Mol2, Mol3, and Mol4, all of them from the chalcone and quinone families. These molecules showed good predicted absorption, distribution, metabolism, and excretion, and toxicity properties. Finally, the molecular dynamics simulation results showed that the three chalcones, Mol1‐4 …
2025-04
Mechanism and stereoselectivity of a [3+ 2] cycloaddition involving a glucosyl nitrone: a MEDT study
Organic & Biomolecular Chemistry (ژمارەی وەرز (Issue) : 20) (بەرگ (Volume) : 23)
In this study, Molecular Electron Density Theory (MEDT) is employed to investigate the reaction mechanism and the experimentally observed stereoselectivity of the [3 + 2] cycloaddition (32CA) between C-(D-glucoso)-N-methyl nitrone 1 and 1H-pyrrole-2,5-dione 2. Within the Conceptual DFT (CDFT) framework, 2 behaves as an electrophile, while 1 acts as the nucleophile. Bonding Evolution Theory (BET) analysis reveals that this 32CA reaction proceeds through a one-step asynchronous mechanism, where the formation of the C3–C4 bond occurs before that of the O1–C5 bond along both the endo and exo pathways. This asynchronous nature is further supported by analyses based on the Electron Localization Function (ELF) and the Quantum Theory of Atoms in Molecules (QTAIM), which confirm the absence of new disynaptic basins (V(C3,C4) and V(O1,C5)) and of new covalent bonds, respectively. Overall, the …
2025-04
Understanding [3+2] cycloaddition reactions of difluoroallene to nitrone and diazoalkanes from the molecular electron density theory perspective
New Journal of Chemistry (ژمارەی وەرز (Issue) : 15) (بەرگ (Volume) : 49)
A detailed theoretical study at the MPWB1K/6-311G(d,p) computational level for the [3+2] cycloaddition (32CA) reactions of 1,1-difluoroallene (DFA) with Z-C-phenyl-N-methyl nitrone (NI), diazomethane (DM) and dimethyl diazomethane (MDM) in the light of molecular electron density theory (MEDT) is herein reported. These 32CA reactions are energetically aligned towards the addition along the non-fluorinated double bond of DFA in each case, in complete agreement with the experiments. The 32CA reactions involving the nitrone and DM were regiospecific, while that of MDM was devoid of any regiochemical control. This could be revealed from the analysis of the corresponding energy profiles for these exergonic kinetically controlled 32CA reactions, following a one-step mechanism via high asynchronous single bond formation processes, also implied by the topological analysis of the electron localization function (ELF) along the more favorable reaction paths. Finally, analysis of the quantum theory of atoms-in-molecules (QTAIM) parameters indicates the absence of any covalent interaction between the two pairs of interacting centers at any transition state structure, which is visualized in the non-covalent interaction (NCI) isosurfaces, in agreement with the ELF analyses.
2025-03
A molecular electron density theory investigation of the mechanism of intramolecular [3+2] cycloaddition (32CA) with the participation of nitrile N-oxide and ethene molecular segments
New Journal of Chemistry (ژمارەی وەرز (Issue) : 15) (بەرگ (Volume) : 49)
In this study, we have investigated the reaction mechanism of the intramolecular [3+2] cycloaddition (32CA) process involving a nitrile oxide-heterocycle system through molecular electron density theory (MEDT). Density functional theory (DFT) calculations at the B3LYP/6-311++G(d,p) level of approximation have been performed to explore both endo and exo stereoisomeric pathways in benzene as a solvent. The results clearly indicate that the exo path is both thermodynamically and kinetically preferred, consistent with experimental findings. This preference is shown by reduced activation energies and greater negative Gibbs free energies for the exo product relative to the endo product. The bonding evolution theory (BET) analysis, in combination with ELF topological analysis, unraveled a stepwise mechanism that involves the formation of nitrogen lone pairs followed by the formation of C–C and C–O bonds. This mechanistic interpretation points out the asynchronicity of the bond-forming process, and the exo pathway is found to be less asynchronous compared to the endo one. Moreover, molecular docking analyses revealed that the exo product has considerable binding affinity to the 1CIN protease, indicating its potential as a therapeutic inhibitor. Moreover, drug-likeness evaluations verified that the compounds adhere to Lipinski's Rule of Five, signifying advantageous pharmacokinetic characteristics. This extensive work combines theoretical and computational approaches to clarify the intricate processes of 32CA reactions, offering significant insights into their synthetic applications and possible medicinal benefits.
2025-03
In-Silico Analysis of Benzo-Selenadiazole Hybrids: Reactivity and Anticancer Potential Assessed Through DFT, Molecular Dynamics, Molecular Docking, and ADMET
Polycyclic Aromatic Compounds (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 45)
Fighting cancer is challenging, but targeting apoptosis pathways offers hope. Caspases 3 and 7 cleave substrates, leading to key features like phosphatidylserine exposure, nuclear condensation, and DNA fragmentation, driving cancer cell death. This understanding aids in developing targeted therapies to selectively eliminate cancer cells. This study explores the synthesis, characterization, and in-silico analysis of carvone-isoxazoline-selenadiazole hybrids (11a–e) as potential anticancer agents. Advanced NMR techniques, including COSY, HSQC, and HMBC, confirmed the structural integrity of the benzo[1–3]selenadiazole core. Among the derivatives, 11c stood out with a low HOMO-LUMO energy gap of 3.2 eV, indicating high reactivity. MEPS analysis revealed biologically active sites at −0.85 and 1.2 eV, while biological evaluations demonstrated 11c’s ability to induce apoptosis via caspase-3 activation with an IC50 of 2.1 μM, similar to doxorubicin. Strong docking interactions with apoptosis-related proteins further support this. Mature caspases 3 and 7 cleave a broad set of substrates, ultimately leading to apoptotic features such as phosphatidylserine exposure, nuclear condensation, and DNA fragmentation. ADMET analysis revealed favorable pharmacokinetics, with a logP of 2.5, and low toxicity risks, with an LD50 value of >1000 mg/kg. Structure-activity relationships highlighted selenium’s pivotal role in enhancing activity. With potent anticancer properties and a promising drug profile, 11c is a compelling candidate for further cancer therapy development.
2025-03
Mechanistic study of N-t-butyl nitrone and cyanoacetylene [3 + 2] cycloaddition: a combined DFT, docking, and ADMET approach
Chemical Monthly (ژمارەی وەرز (Issue) : 2025) (بەرگ (Volume) : 156)
The Molecular Electron Density Theory (MEDT) has been used to study the [3 + 2] cycloaddition (32CA) reaction of an N-t-butyl nitrone with a cyanoacetylene at the B3LYP/6–311 + + G(d,p) computational level. However, the DFT-based reactivity indices show that N-t-butyl nitrone is a strong nucleophile, while cyanoacetylene exhibits strong electrophile properties. The reaction takes place in two paths (a and b). In addition, in the Potential Energy Surface (PES) analysis, energy profiles show that path a is more favorable and more spontaneous, with both products forming through exothermic reactions. Moreover, Bonding Evolution Theory (BET) analysis revealed that these 32CA reactions proceed via the coupling of pseudoradical centers, with the formation of new C–C and C–O covalent bonds occurring only after the transition states (TS). It is interesting to note that, with the electronic flux from the N-t-butyl nitrone to the cyanoacetylene, a low polarity of the forward electron density transfer (FEDF) type is predicted by the global electron density transfer (GEDT) between 0.1169 and 0.14862 e. In particular, in this one-step zw-type 32CA reaction, the atom-in-molecules (AIM) topological characterization of the electron density at the TSs structures and the electron localization function (ELF) are not considered. Certainly, the major cervical intraepithelial neoplasia or (1CIN) protein underwent a docking survey for cycloadducts 2-(tert-butyl)-2,3-dihydroisoxazole-4-carbonitrile and 2-(tert-butyl)-2,3-dihydroisoxazole-5-carbonitrile. The analysis shows that cycloadducts 2-(tert-butyl)-2,3-dihydroisoxazole-4-carbonitrile have higher binding energy, while cycloadducts 2-(tert-butyl)-2,3-dihydroisoxazole-5-carbonitrile have lower binding energy than the co-crystal ligand. Finally, the drug-likeness assessment and ADMET predictions were demonstrated for products 2-(tert-butyl)-2,3-dihydroisoxazole-4-carbonitrile and 2-(tert-butyl)-2,3-dihydroisoxazole-5-carbonitrile. The ADMET analysis of molecule 2-(tert-butyl)-2,3-dihydroisoxazole-4-carbonitrile is the most promising drug-like molecule.
2025-03
Mechanistic study of nitrone and maleimide [3 + 2] cycloaddition: a combined DFT, BET study, docking, and ADMET approach from the MEDT perspective
Structural Chemistry (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 36)
A [3 + 2] cycloaddition (32CA) reaction between maleimide (MD1, MD2) and nitrones (NT1, NT2, NT3) was investigated at the MPWB95/6-311G(d,p) level of theory utilizing Molecular Electron Density Theory (MEDT). Conceptual density functional theory (CDFT) indices substantiated the roles of maleimide (MD1, MD2) and nitrones (NT1, NT2, NT3) as electrophiles and nucleophiles, respectively. The reaction proceeds via two possible pathways: exo and endo. Investigation of the Potential Energy Surface (PES) revealed that the exo and endo pathways exhibit Gibbs free energy values of (− 13.84, − 13.82, − 12.31, − 14.18 kcal·mol-1) and (− 8.78, − 7.87, − 7.88, − 8.54 kcal·mol-1), respectively, indicating kinetically controlled, highly exothermic, and spontaneous reactions, as evidenced by negative ΔG values. The global electron density transfer (GEDT) values ranging from 0.08 to 0.19e suggest a low-polarity electron density transfer of the forward electron density flux (FEDF) type from nitrones (NT1, NT2, NT3) to maleimide (MD1, MD2), while local indices, particularly Parr functions, elucidate the electronic spin distribution. Analyses employing electron localization function (ELF) in conjunction with quantum theory of atoms in molecules (QTAIM) identified the nitrone species as participating in a one-step zw-type 32CA reaction. However, topological analysis of the electron density at the transition state demonstrated that these reactions proceed via a non-concerted mechanism. Bonding Evolution Theory (BET) analysis further elucidated the reaction mechanism, revealing six Structural Stability Domains (SSDs) and pseudoradical centers at the C4–C3 and C5–O1 bonds in the transition states. Molecular docking studies demonstrated that the cycloadducts (IZ1, IZ2, IZ3, and IZ4) exhibited binding energies (− 10.88, − 10.61, − 10.40, and − 11.68 kcal mol-1) with the Michigan Cancer Foundation-7 (MCF-7) protein (3ERT) that were lower than the co-crystal ligand (− 13.10 kcal mol-1). The in silico ADMET and drug-likeness predictions suggest promising potential for further investigation.
2025-02
Quantum evaluation of novel epoxides: molecular docking, dynamics simulation, pharmacokinetics, stereoselectivity, and mechanistic insights into cis-himachalone and cis-himachalol epoxidation
Chemistry of Heterocyclic Compounds (ژمارەی وەرز (Issue) : 11) (بەرگ (Volume) : 60)
The stereoselectivity of the epoxidation reactions of cis-himachalone and cis-himachalol was investigated using theoretical approaches. Density functional theory calculations at the WB97XD/6-311G(d,p) level were employed to analyze chemical reactivity, utilizing reactivity indices within the framework of conceptual density functional theory. This analysis predicts that m-CPBA acts as an electrophile, while cis-himachalone and cis-himachalol function as nucleophiles. Examination of the energies associated with different reaction pathways indicates that the epoxidation reactions exhibit stereoselectivity. Additionally, molecular docking was conducted to target the catalytic domain of the Gram-positive Staphylococcus aureus topoisomerase IV enzyme, demonstrating that tested compounds possess favorable binding affinities compared to novobiocin. To assess the stability and structural characteristics of the protein–ligand complexes, 100-ns molecular dynamics simulations were performed. After analyzing several key parameters, including RMSD, RMSF, Rg, and the number of hydrogen bonds, it was found that tested compounds maintained stable protein conformations similar to those of the reference compound, suggesting their potential as effective inhibitors of the Staphylococcus aureus topoisomerase IV enzyme.
2025-02
Comprehensive study on the stereoselective epoxidation of aromatic atlantone: mechanism, ADME analysis, and potential as COVID-19 drug
Chemistry of Heterocyclic Compounds (ژمارەی وەرز (Issue) : 11) (بەرگ (Volume) : 60)
This work presents a theoretical investigation of the epoxidation reaction of 2-methyl-6-(4-methylphenyl)hept-2-en-4-one using hydrogen peroxide in the presence of sodium hydroxide and ethanol as a solvent. The study was conducted using density functional theory (DFT) with the 6-311G(d,p) basis set. Calculations of activation energies for the transition states revealed the stereoselectivity of the reaction, with theoretical results closely matching experimental data. Additionally, an electronic localization function (ELF) analysis was performed to clarify the reaction mechanism. A docking study was also conducted to predict potential drug candidates against COVID-19.
2025-02
Quantum study of the [3+2] cycloaddition of nitrile oxide and carvone oxime: insights into toxicity, pharmacokinetics, and mechanism
Chemistry of Heterocyclic Compounds (ژمارەی وەرز (Issue) : 11) (بەرگ (Volume) : 60)
he study employs molecular electron density theory (MEDT) to investigate the mechanism of [3+2] cycloaddition involving carvone-based oxime and nitrile oxide. Reactivity indices as well as activation and reaction energies were determined by density functional theory (DFT) calculations employing the B3LYP/6-311(d,p) method. According to a conceptual DFT indices study, carvone-based oxime was characterized as a nucleophile, while the investigated nitrile oxide acts as an electrophile in the reaction. The reaction demonstrates chemoselectivity and regiospecificity, as confirmed by the electron localization analysis and energy evaluations, consistent with experimental observations. Bond evolution theory analysis suggests a one-step two-stage mechanism with asynchronous bond formation. Additionally, docking studies on the possible reaction products reveal enhanced interactions with proteins, attributed to the presence of oxygen and nitrogen atoms, which increase their affinity for the SARS-CoV-2 protease. Furthermore, a docking analysis shows that one of the investigated ligands exhibits strong binding affinity for both HIV-1 and SARS-CoV-2 proteins, indicating a high potential for interaction with these viral targets.
2025-02
Unlocking potential natural products from African sources targeting overexpressed estrogen receptor alpha (ERα) in breast cancer: in silico studies
Computational and Structural Biotechnology Reports (ژمارەی وەرز (Issue) : 2025) (بەرگ (Volume) : 2)
The main goal of this research is to identify natural products from ConMedNP and SANCDB libraries targeting overexpressed estrogen receptor alpha (ERα) in breast cancer using molecular docking and molecular dynamics (MD) methods. A protein (PDB ID: 1G50) was selected for its unique co-crystallized inhibitor 17β-estradiol and a specific binding pocket with amino acid residues conducive to inhibiting agonist activity. After validating the docking protocol, we performed structure-based virtual screening via molecular docking and Molecular Mechanics Generalized Born Surface Area (MM-GBSA) binding affinity calculations, resulting in the identification of 20 hits. We conducted a detailed analysis of the top-scoring molecules using docking and MD simulations. Five molecules (BNG_UY_488, SANC00320, BNG_UY_243, ZTF_UY_260, and SAO_0001_1) emerged as lead candidates, demonstrating better performance than the 17β-estradiol (E2) inhibitor in both docking and MD simulations. Furthermore, we assessed the synthetic feasibility of these five compounds using SwissADME, revealing their ease of synthesis compared to the co-crystallized inhibitor.
2025-02
Computational investigation on [2π + 4π] cycloaddition mechanisms of buta-1,3-diene derivatives with sulfur dioxide: DFT and in silico study
Structural Chemistry (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 36)
The present study explores the [2π + 4π] cycloaddition reaction with the participation of a buta-1,3-diene series with sulfur dioxide. This investigation employs the molecular electron density theory (MEDT), using the 6-311G(d,p) basis set coupled with the MPWB1K method. Analysis of SO2 reactivity reveals a predominance of the monosynaptic basin V(S2) with a population of 3.14 e and asymmetric NBO charges, where sulfur (1.597) acts as an electrophilic site. The study of chemical potentials shows that SO2 (μ = 5.37 eV) reacts with dienes via polar interactions, primarily targeting the nucleophilic carbons C1 and C7. The activation energies, ranging from 10.44 to 14.95 kcal.mol−1, indicate high barriers, with thermodynamically stable products (∆G range from − 7.35 to − 10.45 kcal.mol−1). The ELF and QTAIM results reveal complex electronic reorganizations without covalent bonds at the transition states, highlighting significant non-covalent interactions. Among the products, P3 stands out for its high binding affinity (− 6.6 kcal.mol−1) and promising ADMET profile, suggesting potential applications in molecular modeling and protein interaction, despite CYP1A2 inhibition.
2025-01

2024

Elucidating the mechanism and selectivity of [3 + 2] cycloaddition: a DFT and molecular docking investigation of the reaction of 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide with dimethyl maleate
Structural Chemistry (ژمارەی وەرز (Issue) : 5) (بەرگ (Volume) : 35)
The [3 + 2] cycloaddition (32CA) reactions involving 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide and dimethyl maleate are examined in this study. Molecular electron density theory (MEDT) is applied at the M06-2X/6-311G(d,p) level, coupled with the D3 dispersion correction. The nitronate 1 species are identified as zwitterionic entities through an analysis of the electron localization function (ELF). This 32CA reaction follows an asynchronous one-step mechanism. Conceptual DFT indices are utilized to classify dimethyl maleate as the electrophilic component and the nitronate as the nucleophilic counterpart. The [3 + 2] cycloaddition processes are predominantly governed by kinetic control, as indicated by activation free energies of − 23.6 and − 11.4 kcal.mol−1 for the exo and endo pathways, respectively, aligning with experimental findings. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather polar 32CA reactions. The formation of a pseudoradical center initiates at carbon atoms C3 and C4. A subsequent docking analysis is conducted on cycloadducts 3 and 4 in relation to the main protease of SARS-CoV-2 (6LU7), alongside the co-crystal ligand. The results of this analysis reveal that cycloadducts 3 exhibit higher binding energy, while cycloadducts 4 display lower binding energy compared to the co-crystal ligand. The results confirm that the presence of isoxazolidine ring increases the affinity of the product 3.
2024-09
Synergistic synthesis and computational analysis of novel indazole-2-Pyrone hybrids: Toxicity, Hirshfeld surface insights, and antiviral potential against HIV-1 and Coronaviruses
Journal of Molecular Structure (ژمارەی وەرز (Issue) : 3) (بەرگ (Volume) : 1321)
A novel category of hybrids, termed (Z)-6-methyl-3-(1-((1-(prop‑2-yn-1-yl)-1H-indazol-6-yl)amino)ethylidene)-2H-pyran-2,4(3H)‑dione, was synthesized by reductive coupling of N-alkyl-6-nitroindazoles and 2-pyrone using indium or stannous chloride in tetrahydrofuran (THF) with acetic acid. This process yielded (Z)-2H-pyran-2,4(3H)-diones in satisfactory yields. Each synthesized molecule underwent comprehensive characterization through NMR analysis and X-ray diffraction. Additionally, our investigation incorporates quantum chemical modeling via density functional theory (DFT) at the B3LYP/6–311G(d,p) level, along with molecular docking analysis. An analysis of the Hirshfeld molecular surface was undertaken to characterize the type of intermolecular connections. The percentage contributions, shown in the footprint plot, indicate that H…H interactions (33.0 %) are particularly significant in the constitution of the crystal. The favorable pharmacological properties of compounds 5a and 6a, such as good bioavailability, ability to penetrate the blood-brain barrier, and adherence to the Lipinski rule, make them excellent candidates for therapeutic development.
2024-09
Unveiling the Ro60-Ro52 complex
EXCLI Journal (بەرگ (Volume) : 23)
The coexistence within a subcellular complex of inter-cellular proteins Ro60, responsible for preserving ncRNA quality, and Ro52, involved in intracellular proteolysis, has been a subject of ongoing debate. Employing molecular docking in tandem with experimental methods like Quartz Crystal Microbalance with Dissipation (QCM-D), Proximity Ligation Assay (PLA), and Indirect Immunofluorescence (IIF), we reveal the presence of Ro60 associating with Ro52 within the cytoplasm. This result unveils the formation of a weak transient complex with a Ka ≈ (3.7 ± 0.3) x 106 M-1, where the toroid-shaped Ro60 structure interacts with the Ro52's Fc receptor, aligning horizontally within the PRY-SPRY domains of the Ro52's homodimer. The stability of this complex relies on the interaction between Ro52 chain A and specific Ro60 residues, such as K133, W177, or L185, vital in the Ro60-YRNA bond. These findings bridge the role of Ro60 in YRNA management with Ro52's function in intracellular proteolysis, emphasizing the potential impact of transient complexes on cellular pathways.
2024-08
Identification of potential dipeptidyl peptidase IV inhibitors from the ConMedNP library by virtual screening, and molecular dynamics methods
Heliyon (ژمارەی وەرز (Issue) : 15) (بەرگ (Volume) : 10)
In this study, we screened novel dipeptidyl peptidase IV (DPP4) inhibitors from the ConMedNP library consisting of 3507 molecules. Interestingly, molecular docking, ADMET, and the anti-diabetic activity predictions suggest that three molecules, namely OTH_UD_XX06_1, GB19, and BMC_000104, have a high binding affinity toward DPP4. The molecular dynamics (MD) simulation results suggest that these hit molecules have a stable binding pose and occupy the binding pockets throughout the 200 ns simulation. The presence of intermolecular H-bonding between the ligands and DPP4 was observed throughout the simulation period. Thus, docking and MD results, predicted that the three compounds were the most potent DPP4 inhibitors that could putatively bind to the DPP4 active site via both conventional H-bonding and hydrophobic interactions. These results could aid the discovery of new drugs to treat type 2 diabetes.
2024-08
Molecular docking, expounding the chemo-, regio-selectivity, and the mechanism of [3+ 2] cycloloaddition reaction between nitrile-imine and (thio)-chalcone
Chemical Monthly (ژمارەی وەرز (Issue) : 6) (بەرگ (Volume) : 155)
The study explores the application of molecular electron density theory, focusing on the [2 + 3] cycloaddition mechanisms between nitrile-imine and chalcone or thiochalcone. Density Functional Theory (DFT) calculations employing the B3LYP/6–311(d,p) methodology are utilized to determine activation and reaction energies, as well as reactivity indices. Through investigation of conceptual DFT indices, nitrile-imine is identified as a nucleophile, while chalcone and thiochalcone act as electrophiles in the reaction. The reactions exhibit both chemo- and regiospecifics, as confirmed by Parr functions, Electron Localization Function (ELF) survey, and energetic analysis, consistent with experimental results. ELF analysis suggests a two-phase mechanism for these [2 + 3] cycloadditions. Furthermore, docking studies on the resultant products reveal enhanced interaction energies with proteins due to the presence of oxygen and sulfur atoms, in their interaction with the crystal structure of COVID-19 main protease (PDB ID: 6LU7) and paves a ways for manufacturing innovation.
2024-06
Unveiling the mechanism and selectivity of the [3 + 2] cycloaddition reactions of nitrone with acetylene derivatives leading to anticancer 4-isoxazoline derivatives from the MEDT perspective
Computational and Theoretical Chemistry (ژمارەی وەرز (Issue) : 5) (بەرگ (Volume) : 1237)
The [3 + 2] cycloaddition reactions of N-methyl-C-(2-furyl) nitrone (a) with a series of acetylene derivatives (4b), (5b), and (6b) have been studied at the B3LYP-D3/6-31G(d) computational level within the framework of Molecular Electron Density Theory. Topological analysis allows classifying the nitrone (a) as a zwitterionic (zw-) three-atom component (TAC) associated with high energy barrier. These 32CA reactions follow a one-step mechanism under kinetic control with highly asynchronous bond formation. Bonding Evolution Theory (BET) analysis indicates that no new covalent Csingle bondO and Csingle bondC bonds form at the transition states (TSs). Interestingly, the global electron density transfer (GEDT) between 0.08 and 0.18 e predicts low polar character of forward electron density transfer (FEDF) type with the electronic flux from the nitrone (a) to the acetylene derivatives. Electron localization function (ELF) and atom-in-molecules (AIM) topological analysis of the electron density at the TS structures characterize the non-concerted nature of these one-step zw-type 32CA reactions.
2024-05
Exploring the synthesis and application of a pyrazole derivative in corrosion protection: Theoretical modeling and experimental investigations
Journal of Molecular Structure (بەرگ (Volume) : 1312)
This research investigates the inhibitory performance of BM-02, a synthesized pyrazole derivative (R)-5-(4-methoxyphenyl)-1,3-diphenyl-4,5-dihydro-1H-pyrazole, against the corrosion of mild steel in a 1 M hydrochloric acid solution. A comprehensive array of experimental techniques, including weight loss analysis, potentiodynamic polarization, electrochemical impedance spectroscopy, and scanning electron microscopy, were employed to assess the inhibitory effectiveness. BM-02 is identified as a mixed inhibitor, showcasing a remarkable efficiency of 91.5 % at a concentration of 10−3 mol/l. The adsorption behavior of the BM-02 molecule was investigated, revealing a physical adsorption model in accordance with the Langmuir isotherm. Furthermore, ATR-IR, 1H NMR, and 13C NMR spectra were acquired, complemented by density functional theory (DFT) calculations and molecular dynamics (MD) simulations to gain deeper insights into the molecular interactions and corrosion inhibition mechanism.
2024-05
Unveiling [3+ 2] cycloaddition reactions of diphenyl diazomethane to thiobenzophenone and cycloaliphatic thioketones in the light of molecular electron density theory
Computational and Theoretical Chemistry (بەرگ (Volume) : 1237)
The reactivity, regiochemistry and substituent effects observed in the [3 + 2] cycloaddition (32CA) reactions of diphenyldiazomethane (PDM) with thiobenzophenone and a series of cycloaliphatic thioketones (TKs) have been studied within the molecular electron density theory at the ωB97XD/6-311G(d,p) computational level. The cycloaliphatic TK series shows remarkable substituent effects, changing from a non-polar 32CA reaction to a highly polar one, with the electron density flowing from PDM to the corresponding TK in a reaction classified as a forward electron density flux (FEDF). These 32CA reactions follow a one-step mechanism through earlier asynchronous transition state structures in which the formation of the two new single bonds has not yet begun, and the energetically predicted regiochemistry towards the generation of 1,3,4-thiadiazole is in complete agreement with the experimental outcome.
2024-05
Synthesis, X-ray analysis, and antiviral evaluation of allohimachalol: Insights into stereoselectivity in epoxidation
Journal of Molecular Structure (ژمارەی وەرز (Issue) : 5) (بەرگ (Volume) : 1305)
Allohimachalol, a vital element in Atlas cedar wood essential oil, is obtained through steam distillation, shaping the oil's distinctive aroma. Its prominence enhances the unique olfactory character of cedar oil, making it valuable in perfumery and aromatherapy. To enhance its reactivity, we conducted experimental and theoretical studies on the epoxidation reaction of Allohimachalol with meta-chloroperbenzoic acid (m-CPBA). This reaction led to the formation of a new product, referred to as product 3, through a simultaneous rearrangement process. The compound structures were identified using spectroscopic techniques, including 1H and 13C NMR, along with X-ray diffraction. Furthermore, the electronic structures of the synthesized compounds were investigated through theoretical calculations using density functional theory (DFT) at the B3LYP/6-311G(d,p) level. The analysis of energy profiles related to different reaction pathways produced results in line with the experimental observations, confirming the alignment of the allohimachalol epoxidation reaction with theoretical predictions. Additionally, a docking analysis was performed on the investigated compounds within the primary protease of SARS-CoV-2 (6LU7) and HIV, indicating that compound 3 holds promise as a potential antiviral drug for human health.
2024-02
A molecular electron density theory study to understand intramolecular [3 + 2] cycloaddition reactions of azides and diazoalkanes
Structural Chemistry (ژمارەی وەرز (Issue) : 6) (بەرگ (Volume) : 34)
The intramolecular [3 + 2] cycloaddition (IM32CA) reactions of azides and diazoalkanes leading to fused tricyclic 1,2,3-triazolines and 1-pyrazolines have been studied at the MPWB1K/6-311G(d,p) computational level within the molecular electron density theory (MEDT). The IM32CA reactions of azides are classified as zw- type following non-concerted one-step mechanism with earlier N1-C5 bond formation implied from the bonding evolution theory (BET) study with the Gibbs free activation energies between 26.3–30.0 kcal mol−1 at 298 K in benzene while that of the diazoalkanes are classified as pmr- type with the earlier C3-C5 bond formation and Gibbs free activation energies between 24.7–29.1 kcal mol−1 at 298 K in n-pentane. The influence of substituent effects on these IM32CA reactions is studied. Azide reactions with minimal global electron density transfer (GEDT) are classified as the null electron density flux (NEDF) while that of the diazoalkanes are classified as forward electron density flux (FEDF). QTAIM analysis and ELF study allow revealing the non-covalent interactions at the TSs.
2024-01

2023

Diastereoselective green synthesis of pyrrolo[1,2-a]quinolines via [3+2] cycloaddition reaction: insights from molecular electron density theory
Theoretical Chemistry Accounts (ژمارەی وەرز (Issue) : 12) (بەرگ (Volume) : 142)
The [3+2] cycloaddition (32CA) reaction between cyclic azomethine ylide (generated from N-phenacylquinolinium bromide) and N-arylmaleimide, leading to pyrrolo[1,2-a]quinolone, has been investigated using the Molecular Electron Density Theory at the B3LYP/6-311++G(d,p) computational level with D3 correction. This study focuses on the zwitter-ionic type 32CA reaction, highlighting its polar character with the electronic flux from the azomethine ylide to the alkene. The reaction proceeds with complete endo-stereoselectivity, and the activation parameters show minimal variations in different solvents, consistent with experimental observations. The activation energy is associated with the depopulation of the N2–C1 and C4–C5 bonding regions, formation of non-bonding electron density at N2 nitrogen and creation of pseudoradical centers at C3, C4 and C5. These findings suggest that the formation of new covalent bonds does not occur at the transition states, in line with the presence of non-covalent interactions at the interatomic bonding regions, as revealed by the topological analysis of the Quantum Theory of Atoms-in-Molecules.
2023-11
Unveiling the mechanism, regiochemistry and substituent effects of the [3 + 2] cycloaddition reactions of C, N-diaryl nitrile imine to ethylene derivatives from the molecular electron density theory perspective
Computational and Theoretical Chemistry (بەرگ (Volume) : 1230)
The [3 + 2] cycloaddition (32CA) reactions of C-(4-methoxyphenyl)-N-phenyl nitrile imine (NI) with a series of ethylene derivatives of increased electrophilic character have been studied within the framework of Molecular Electron Density Theory (MEDT). These 32CA reactions are kinetically controlled with activation Gibbs free energies between 14.8 and 24.0 kcal mol−1, and with the preferred regioselectivity involving the nucleophilic attack of the carbenoid carbon of NI on the non-substituted carbon of the electrophilic ethylenes in agreement with the experimental outcomes. The presence of electron-withdrawing substituents in the ethylene makes the 32CA reaction of forward electron density flux (FEDF) more quickly, relative to that with nucleophilic propene, showing the highest activation parameters and non-polar character. Electron localization function (ELF) and atom-in-molecules (AIM) topological analysis of the electron density at the transition state structures characterize the non-concerted nature of these one-step cb-type 32CA reactions.
2023-11
Investigation of the molecular mechanism and diastereoselectivity in the [3 + 2] cycloaddition reaction between acetonitrile oxide and Cis-3,4-Dichlorocyclobutene: Insights from MEDT and docking study
Computational and Theoretical Chemistry (بەرگ (Volume) : 1228)
[3 + 2] cycloaddition (32CA) reactions involving acetonitrile oxide 1 and cis-3,4-dichlorocyclobutene 2 has been investigated via Molecular Electron Density Theory (MEDT) at B3LYP and M06-2X associated with the basis 6–311++G(d,p). The calculated energy profile demonstrates clearly that this reaction is considerably high diastereoselectivity, which is perfectly in accordance with the results of the experiments. The cycloaddition reaction's molecular mechanism has been examined in bonding evolution theory (BET) terms that displays several changes in electron densities along the reaction pathway and demonstrates a one-step process with highly asynchronous transition states. The acetonitrile oxide under study was classified as zwitter-ionic species from the topological analysis of the electron localization function (ELF). In addition, the optimum solvent for performing this cycloaddition is cyclohexane, which is followed by ether and then chloroform. In a further step, a docking survey was carried out for cycloadducts 3, 3-F, 4 and 4-F docked to the main protease of SARS-CoV2 (6LU7) in comparison with ribavirin, revealing that these cycloadducts have lower binding energies than ribavirin.
2023-08
Theoretical insight into the mechanism and selectivity of the [3 + 2] cycloaddition reaction of N-methyl-1-phenylmethanimine oxide and bicyclopropylidene from the MEDT perspective
Structural Chemistry (ژمارەی وەرز (Issue) : 4) (بەرگ (Volume) : 34)
The mechanism and regioselectivity of [3 + 2] cycloaddition (32CA) reactions of N-methyl-1-phenylmethanimine oxide nitrone 1 and bicyclopropylidene 2 are analyzed using molecular electron density theory (MEDT) at the B3LYP/6–311 + + G(d,p) level. A study of the electron localisation function (ELF) predicts the zwitter-ionic nature of the nitrone, allowing its participation in zw-type 32CA reactions with a high energy barrier that must be surmounted by suitable electrophilic–nucleophilic interactions. The global electronic flux from the strong nucleophilic bicyclopropylidene 2 to the electrophilic nitrone 1 is predicted by an analysis of the CDFT indices. In this 32CA reaction, no new covalent bonds are generated at the TSs, and the mechanism is one-step and kinetically controlled with low asynchronicity in bond formation. The Gibbs free energy of this 32CA reaction in the gas phase is −9.88 and −15.01 kcal.mol−1 for exo and endo path, respectively. The increased thermodynamic stability of the cycloadducts 4 favors the endo regiochemical route. The ELF topological examination at the transition states is in agreement with the predictions of bonding evolution theory (BET) for the endo and exo routes, which point to a one-step process including early transition states.
2023-07
Unveiling the Stereoselectivity and Regioselectivity of the [3+ 2] Cycloaddition Reaction between N-methyl-C-4-methylphenyl-nitrone and 2-Propynamide from a MEDT Perspective
International Journal of Molecular Sciences (ژمارەی وەرز (Issue) : 10) (بەرگ (Volume) : 24)
[3+2] cycloaddition reactions play a crucial role in synthesizing complex organic molecules and have significant applications in drug discovery and materials science. In this study, the [3+2] cycloaddition (32CA) reactions of N-methyl-C-4-methyl phenyl-nitrone 1 and 2-propynamide 2, which have not been extensively studied before, were investigated using molecular electron density theory (MEDT) at the B3LYP/6–311++G(d,p) level of theory. According to an electron localization function (ELF) study, N-methyl-C-4-methyl phenyl-nitrone 1 is a zwitterionic species with no pseudoradical or carbenoid centers. Conceptual density functional theory (CDFT) indices were used to predict the global electronic flux from the strong nucleophilic N-methyl-C-4-methyl phenylnitrone 1 to the electrophilic 2-propynamide 2 functions. The 32CA reactions proceeded through two pairs of stereo- and regioisomeric reaction pathways to generate four different products: 3, 4, 5, and 6. The reaction pathways were irreversible owing to their exothermic characters: −136.48, −130.08, −130.99, and −140.81 kJ mol−1, respectively. The enthalpy of the 32CA reaction leading to the formation of cycloadduct 6 was lower compared with the other path owing to a slight increase in its polar character, observed through the global electron density transfer (GEDT) during the transition states and along the reaction path. A bonding evolution theory (BET) analysis showed that these 32CA reactions proceed through the coupling of pseudoradical centers, and the formation of new C-C and C-O covalent bonds did not begin in the transition states.
2023-05
Unveiling substituent effects in [3+ 2] cycloaddition reactions of benzonitrile N-oxide and benzylideneanilines from the molecular electron density theory perspective
Scientiae Radices (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 2)
The zw-type [3+ 2] cycloaddition (32CA) reactions of benzonitrile N-oxide with a series of substituted benzylideneanilines have been studied within the Molecular Electron Density Theory (MEDT) at the B3LYP/6-31G (d) computational level. The presence of dimethylamino and methoxy substituents in the aromatic rings of benzylideneaniline makes the reaction more facile relative to the unsubstituted one, while the electron withdrawing nitro substituents relatively induce minimal changes in the energy profile complying with the experimentally observed reaction rates. The presence of nonbonding electron density at the nitrogen atom and the formation of pseudoradical centre at the carbon atom of benzonitrile N-oxide characterise the difference in electronic structure of the TSs relative to the reagents, while the topological analysis of the electron localization function (ELF) and the atoms-in-molecules (AIM) reveal no covalent bond formation at the early TSs. The present MEDT study analyses the experimentally observed substituent effects and complete regioselectivity in the studied 32CA reactions.
2023-03

2022

Unveiling [3+ 2] cycloaddition reactions of N-methyl-C-3-bromophenyl-nitrone to dimethyl maleate: molecular electron density theory perspective
Journal of the Mexican Chemical Society (ژمارەی وەرز (Issue) : 4) (بەرگ (Volume) : 66)
The zwitterionic-type (zw-type)[3+ 2] cycloaddition (32CA) reactions of N-methyl-C-3-bromophenyl-nitrone 1 with dimethyl maleate 2 with increased electrophilicity were investigated using the Molecular Electron Density Theory (MEDT) at the MPWB95/6-311++ G (d, p) computational level. Both reactivity and selectivity are rationalized in relation to the polarity of the reaction. The associated zw-type 32CA reactions are accelerated due to the high nucleophilic character of N-methyl-C-3-bromophenyl-nitrone 1 and the strong electrophilic character of dimethyl maleate 2, which also play a critical part in the mechanism of the reaction, influencing the stereoselectivity, with activation enthalpies in between 34.04 and 38.37 kJ. mol-1 in the gas phase. The CDFT indices are used to anticipate global electron density flux from the nucleophilic N-methyl-C-3-bromophenyl-nitrone 1 to the electrophilic dimethyl maleate 2. These exergonic 32CA reactions have negative Gibbs free energy along the endo and exo stereochemical pathways. The endo stereochemical process is preferred over the exo stereochemical pathway in this kinetically controlled 32CA reaction. The predictions of bonding evolution theory (BET) for the endo and exo pathways indicate a one-step process with early transition states, which is compatible with the ELF topological examination of transition states.
2022-12
Insights into the mechanism and stereoselectivity of the [3+2] cycloaddition reaction between N‑methyl‑C‑(4‑hydroxylphenyl) nitrone and maleic anhydride with a molecular electron density theory perspective
Theoretical Chemistry Accounts (ژمارەی وەرز (Issue) : 33) (بەرگ (Volume) : 141)
The [3+2] cycloaddition (32CA) reaction of N-methyl-C-(4-hydroxylphenyl) nitrone 1 and maleic anhydride 2 has been investigated using molecular electron density theory (MEDT) at the MPWB95/6-311++G(d,p) computational level. This 32CA reaction undergoes two stereo- and stereoisomeric reaction paths to form two different products 3 and 4. An electron localization function (ELF) study predicts that the N-methyl-C-(4 hydroxylphenyl) nitrone 1 has a zwitterionic character and it takes place through a one-step mechanism, with activation enthalpies in between 17.48 and 23.41 kJ mol−1 in the gas phase. The CDFT indices are used to forecast the global electron density flux from the strong nucleophilic N-methylC-(4-hydroxylphenyl) nitrone 1 to the electrophilic maleic anhydride 2. These exergonic 32CA reactions have negative Gibbs free energy along the endo and exo stereochemical routes. The endo stereochemical process is favored over the exo stereochemical pathway due to the increased thermodynamic stability of the cycloadduct. Bonding evolution theory (BET) predictions for the endo and exo routes indicate a one-step process with early transition states, which is consistent with the ELF topological investigation at the transition states.
2022-06
Unveiling the synthesis of spirocyclic, tricyclic, and bicyclic triazolooxazines from intramolecular [3 + 2] azide-alkyne cycloadditions with a molecular electron density theory perspective
Structural Chemistry (بەرگ (Volume) : 33)
The intramolecular [3+2] cycloaddition (32CA) reactions of azido alkynes leading to spirocyclic, tricyclic, and bicyclic triazolooxazines has been studied within the molecular electron density theory (MEDT) at the MPWB1K/6-311G(d,p) level. The electron localization function (ELF) characterizes the azido alkynes as zwitterionic species. Analysis of the conceptual DFT indices allows classifying the azide moiety as the electrophilic counterpart and the alkyne as the nucleophilic one. These 32CA reactions are under kinetic control with the activation free energies of 23.4–26.7 kcal mol−1. Along the reaction path, the pseudoradical centre is created initially at C4, consistent with the Parr function analysis; however, the sequence of bond formation is controlled by the energetically feasible formation of the six-membered oxazine ring. The intermolecular interactions at the transition states were characterized from the quantum theory of atoms in molecules (QTAIM) study and the non-covalent interaction (NCI) gradient isosurfaces.
2022-01

2021

Unveiling the regioselective synthesis of antiviral 5-isoxazol-5-yl-2'deoxyuridines with a molecular electron density theory perspective
Journal of the Serbian Chemical Society (ژمارەی وەرز (Issue) : 12) (بەرگ (Volume) : 86)
The regioselective synthesis of a potent antiviral sugar nucleoside isoxazole analogue from the 32CA reaction of acetonitrile-N-oxide (ANO) and acetyl-protected 5-ethynyl-2-deoxyuridine (EDU) has been studied at MPWB1K/6-311G (d, p) level within the molecular electron density theory (MEDT) perspective. ANO is classified as a zwitter-ionic species devoid of any pseudoradical or carbenoid centre from the electron localization function (ELF) analysis. The ortho regioisomer is energetically preferred over the meta one by the activation enthalpy of 5.2-5.8 kcal mol-1, suggesting complete regioselectivity in agreeement with the experiment. The activation enthalpy increases from 12.9 kcal mol-1 in gas phase to 17.1 kcal mol-1 in water suggesting more facile reaction in non-polar solvents. The minimal global electron density transfer (GEDT) at the TSs suggest non-polar character and the formation of new covalent bonds has not been started at the located TSs showing non-covalent intermolecular interactions from Atoms-in Molecules (AIM) study and in the Independent Gradient Model (IGM) isosurfaces. The AIM analysis shows more accumulation of electron density at the CC bonding region relative to the CO one, and earlier CC bond formation is predicted from the bonding evolution theory (BET) study.
2021-12
Ab initio Study of Diels-Alder Reaction between Cyclic Dienes and Olefin
Asian Journal of Applied Chemistry Research (ژمارەی وەرز (Issue) : 3) (بەرگ (Volume) : 9)
Theoretical modeling of organic synthesis is a powerful tool and leads to further insight into chemical systems. Computational chemistry allows obtaining the potential energy surface that experimentally cannot be observed, in addition to transition state calculations, which lead to better understanding the reactivity of an organic synthesis work. The Diels-Alder (DA) reaction of cyclopentadiene 1 and N-phenylmaleimide 2 has been studied at the MP2/6-311++G(d,p) level of theory. This DA reaction occurs through a one-step mechanism. It was expected that this reaction undergoes two regio-isomeric reaction paths passing through two different transition states to form two different products 3 and 4. The reaction paths are irreversible due to the exothermic character of -41.24 and -41.73 kcal.mol-1. This DA reaction are exergonic with reactions Gibbs free energies between -27.26 and -27.74 kcal⋅mol−1. Analysis of the CDFT indices predict the global electronic flux from the strong nucleophilic cyclopentadiene 1 to the electrophilic N-phenylmaleimide 2.
2021-09
Theoretical Study of The Reaction of Ketene with Methanimine Using DFT Method
Zanco Journal of Pure and Applied Sciences (ژمارەی وەرز (Issue) : 4) (بەرگ (Volume) : 33)
The Density Functional Theory (DFT) method was used to investigate the stepwise mechanism of the [2+ 2] cycloaddition (22CA) reaction of ketene with methanimine at the B3LYP/6-311++ G (d, p) level of theory. Two modes of attack between reactants were investigated, yielding Azetidin-2-one from path1 and Azetidin-2-one from path2 as two possible products passing through two different transition states. The geometry of transition states and products was analysed. The study of stationary points and energetic parameters shows that the reaction mechanism is stepwise and that Azetidin-2-one P1 is thermodynamically and kinetically more favoured than Azetidin-3-one P2. The analysis of the frontier molecular HOMO and LUMO orbitals shows that the Azetidin-2-one P1 is more stable due to its higher energy gab. The global electronic flux from the strong nucleophilic ketene R1 to the methanimine R2 is predicted using conceptual density functional theory (CDFT) indices. Reactant’s electrophilic and nucleophilic Fukui functions were also investigated.
2021-08
A molecular electron density theory study of the [3+ 2] cycloaddition reaction of nitronic ester with methyl acrylate
Theoretical Chemistry Accounts (ژمارەی وەرز (Issue) : 7) (بەرگ (Volume) : 140)
The [3 + 2] cycloaddition (32CA) reaction of nitronic ester with methyl acrylate has been studied within the molecular electron density theory to analyse the mechanism and experimentally observed regioselectivity. Electron localisation function (ELF) study predicts zwitter-ionic character of the nitrone, allowing its participation in zw-type 32CA reactions associated with high energy barrier demanding overcome through appropriate electrophilic–nucleophilic interactions. Analysis of the CDFT indices predict the global electronic flux from the strong nucleophilic nitrone to the electrophilic methyl acrylate. These 32CA reactions are exergonic with negative reactions Gibbs free energies along ortho regiochemical pathway. Among the ortho and meta regiochemical pathways, ortho path is preferred owing to the higher thermodynamic stability of the cycloadducts. Bonding evolution theory (BET) study predicts one-step mechanism with early transition states for the ortho and meta pathways, in conformity with the ELF topological study at the transition states.
2021-07
Unveiling [3+ 2] cycloaddition reactions of benzonitrile oxide and diphenyl diazomethane to cyclopentene and norbornene: a molecular electron density theory perspective
Theoretical Chemistry Accounts (ژمارەی وەرز (Issue) : 8) (بەرگ (Volume) : 140)
A molecular electron density theory (MEDT) study is performed for the [3 + 2] cycloaddition (32CA) reactions of benzonitrile oxide (BNO) and diphenyldiazomethane (DPDM) to cyclopentene (CP) and norbornene (NBN) with the objective to analyse the experimentally observed acceleration in NBN reactions relative to the CP ones. The activation enthalpy of the 32CA reaction of NBN with BNO is lowered than that of CP by 2.1–2.9 kcal mol−1 in gas phase, DMSO, acetonitrile and THF, while the corresponding differences are 1.3–1.8 kcal mol−1 with DPDM. The 32CA reactions of DPDM show lower activation parameters compared to that of BNO consistent with the respective pseudo(mono)radical and zwitterionic type characters of DPDM and BNO. The syn diastereofacial approach of NBN is energetically feasible compared to the anti one. The global electron density transfer (GEDT) is identified to …
2021-07
Understanding the Reactivity of C-Cyclopropyl-N-Methylnitrone Participating in [3+2] Cycloaddition Reactions Towards Styrene with a Molecular Electron Density Theory Perspective
Journal of the Mexican Chemical Society (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 65)
The [3+2] cycloaddition (32CA) reactions of C-cyclopropyl-N-methylnitrone 1 with styrene 2 have been studied within molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) level of theory. These zwitterionic type 32CA reactions occur through a one-step mechanism. The 32CA reactions undergo four stereo- and regioisomeric reaction paths to form four different products, 3, 4, 5 and 6. Analysis of the conceptual density functional theory (CDFT) indices predict the global electronic flux from the strong nucleophilic nitrone 1 to the styrene 2. These 32CA reactions are endergonic with reactions Gibbs free energies between 2.83 and 7.39 kcal.mol-1 in the gas phase. The 32CA reaction leading to the formation of cycloadduct 3 presents the lowest activation enthalpy than the other paths due to a slightly increase in polar character evident from the global electron density transfer (GEDT) at the transition states and along the reaction path. The bonding evolution theory (BET) study suggests that these 32CA reactions occur through the coupling of pseudoradical centers and the formation of new C-C and C-O covalent bonds has not been started in the transition states.
2021-01
Insights into the mechanism and regioselectivity of the [3+2] cycloaddition reactions of cyclic nitrone to nitrile functions with a molecular electron density theory perspective
Theoretical Chemistry Accounts (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 140)
A molecular electron density theory study is presented for [3 + 2] cycloaddition (32CA) reactions of 2,2-dimethyl-1-pyrroline-1-oxide with the nitrile functions to analyse the mechanism and experimentally observed regioselectivity. Electron localisation function (ELF) study predicts zwitter-ionic character of the cyclic nitrone, allowing its participation in zw-type 32CA reactions associated with high energy barrier demanding overcome through appropriate electrophilic–nucleophilic interactions. Analysis of the CDFT indices predict the global electronic flux from the strong nucleophilic nitrone to the electrophilic nitrile functions. These 32CA reactions are endergonic with reactions Gibbs free energies between 5.5 and 39.2 kcal⋅mol−1 in toluene. The ortho regiochemical pathway is preferred owing to the higher thermodynamic stability of the 2,3-dihydro-1,2,4-oxadiazole derivatives. The 32CA reaction of the nitrile function with carbomethoxy substituent is more facile relative to that with the phenyl substituent. Bonding evolution theory study predicts one-step mechanism with early TSs for the ortho pathway, while a one-step-two-stage mechanism is predicted for the meta reaction path, in conformity with the ELF and AIM topological studies at the TSs.
2021-01
Unveiling the high regioselectivity and stereoselectivity within the synthesis of spirooxindolenitropyrrolidine: A molecular electron density theory perspective
Journal of Physical Organic Chemistry (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 34)
A molecular electron density theory (MEDT) study for the [3 + 2] cycloaddition (32CA) reaction of indoledione and N‐methyl glycine with (E)‐1‐bromonitrostyrene leading to the spirooxindole‐pyrrolidine adduct is presented. Electron localisation function (ELF) study of the in situ generated azomethine ylide classifies a pseudodiradical electronic structure associated with low activation energies. This 32CA reaction is a polar process with electronic flux from the strongly nucleophilic azomethine ylide to the strongly electrophilic nitrostyrene, confirmed from the global electron density transfer (GEDT) above 0.20 e at the transition states (TSs). Parr function analysis predicts the correct regioselectivity from the two‐centre interactions. The reaction is kinetically controlled with negative free energy of reaction which makes it irreversible. The activation enthalpy of the favoured TS is lowered by 3.4, 6.3 and 9.3 kcal mol−1 in methanol relative to the other feasible reaction paths, consistent with the experimentally observed complete regioselectivity and stereoselectivity. ELF topological characterisation along the reaction path predicts a two‐stage one‐step molecular mechanism, and bond formation is controlled by the nucleophilic character of the azomethine ylide. ELF study, Laplacian of electron density and independent gradient model (IGM) analysis predict non‐covalent interactions at the TSs, where the new C–C bond formation has not been started.
2021-01

2020

A Molecular Electron Density Theory Study for [3+2] Cycloaddition Reactions of N-Benzylcyclohexylnitrone with Methyl-3- butenoate
New Journal of Chemistry
The [3+2] cycloaddition (32CA) reactions of N-benzylcyclohexylnitrone 1 with methyl-3-butenoate 2 have been studied within molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) level of theory. These zwitterionic type 32CA reactions occur through a one-step mechanism. The 32CA reactions undergo two pairs of stereo- and regioisomeric reaction paths to form four different products, 3, 4, 5 and 6. The reaction paths are irreversible due to the exothermic character of −18.5 and −12.4 kcal mol−1. The 32CA reaction leading to the formation of cycloadduct 3 presents the lowest activation enthalpy compared to the other path due to a slight increase in polar character evident from the global electron density transfer (GEDT) at the transition states and along the reaction path. The bonding evolution theory (BET) study suggests that these 32CA reactions occur through the coupling of pseudoradical centers and the formation of new C–C and C–O covalent bonds has not been started in the transition states.
2020-11
U nderstanding the Reactivity of Trimethylsilyldiazoalkanes Participating in [3+2] Cycloaddition Reactions towards Diethylfumarate with a Molecular Electron Density Theory Perspective
Organics (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 1)
A Molecular Electron Density Theory (MEDT) study is presented here for [3+2] cycloaddition (32CA) reactions of three trimethylsilyldiazoalkanes with diethyl fumarate. The presence of silicon bonded to the carbon of these silyldiazoalkanes changes its structure and reactivity from a pseudomonoradical to that of a zwitterionic one. A one-step mechanism is predicted for these polar zw-type 32CA reactions with activation enthalpies in CCl4 between 8.0 and 19.7 kcal·mol−1 at the MPWB1K (PCM)/6-311G(d,p) level of theory. The negative reaction Gibbs energies between −3.1 and −13.2 kcal·mole−1 in CCl4 suggests exergonic character, making the reactions irreversible. Analysis of the sequential changes in the bonding pattern along the reaction paths characterizes these zw-type 32CA reactions. The increase in nucleophilic character of the trimethylsilyldiazoalkanes makes these 32CA reactions more polar. Consequently, the activation enthalpies are decreased and the TSs require less energy cost. Non-covalent interactions at the TSs account for the stereoselectivity found in these 32CA reactions involving the bulky trimethylsilyl group.
2020-10
A molecular electron density theory study for [3 + 2] cycloaddition reactions of 1‐pyrroline‐1‐oxide with disubstituted acetylenes leading to bicyclic 4‐isoxazolines
International Journal of Quantum Chemistry (ژمارەی وەرز (Issue) : 3) (بەرگ (Volume) : 121)
The [3 + 2] cycloaddition (32CA) reactions of 1‐pyrroline‐1‐oxide with acetylene and with a series of four symmetrically disubstituted acetylenes (XC ≡ CX, X = CH3, NH2, OH, F), leading to 4,5‐disubstituted bicyclic 4‐isoxazolines, have been studied within molecular electron density theory at the B3LYP‐D3/6‐311++G(d,p) computational level. These 32CA reactions take place through a one‐step mechanism, with activation enthalpies in toluene between 24.4 (X = NH2) and 12.9 (X = F) kcal mol−1. Due to the strong exergonic character of these 32CA reactions, between −12.0 and −47.6 kcal mol−1, they are irreversible. The 32CA reaction of difluoroacetylene, involving fluorine as the most electronegative atom of this series attached to the acetylene carbons, presents the lowest activation enthalpy due to the increase of the polar character of this 32CA reaction, evidenced by the analysis of the global electron density transfer at the corresponding transition state structure. The topological analysis of the electron localization function along the reaction paths of these 32CA reactions allows us to characterize them as the zwitterionic‐type ones. The formation of the new C-C and C-O single bonds takes place at the end of the reactions through the coupling of pseudoradical centers.
2020-10
Insights into the mechanism and regiochemistry of the 1,3-dipolar cycloaddition reaction between benzaldehyde and diazomethane
Theoretical Chemistry Accounts volume (ژمارەی وەرز (Issue) : 9) (بەرگ (Volume) : 139)
The 1,3-dipolar cycloaddition reaction of benzaldehyde with diazomethane is investigated, in gas phase and in diverse polar solvents, using the molecular electron density theory through density functional theory calculations at the B3LYP(+D3)/6-31G(d) level. Analysis of the reaction pathway reveals that this reaction takes place along a concerted but asynchronous mechanism. Computations show that the acetophenone product is kinetically and thermodynamically more favored than 2-phenylacetaldehyde product in agreement with experimental outcomes. The favored cyclization mode and the observed regioselectivity of this cycloaddition are rationalized by both activation energy calculations, frontier molecular orbital analysis and reactivity indices. Also, polar solvents effect favors the reaction. Furthermore, we performed electron localization function (ELF) topological analysis. The ELF topological analysis of diazomethane indicates that this reactant presents an allenic pseudoradical electronic structure.
2020-08
Oxygen Functionalized and Pristine Carbon Nanotubes Efficiency for Adsorption of Methyl Orange Dye
International Research Journal of Pure and Applied Chemistry (ژمارەی وەرز (Issue) : 7) (بەرگ (Volume) : 21)
Pristine and oxygen functionalized multi-walled carbon nanotubes were used as adsorbent for removal of Methyl Orange (MO) dye. The adsorption was carried out under different pH values. The analysis of results indicated that the adsorption characteristics of the MO dye by pristine carbon nanotubes (P-CNTs) and oxygen functionalized carbon nanotubes (O2-CNTs) are highly influenced by the pH of the medium. The study report that the best pH medium of solution for the adsorption of MO on both CNTs was acid medium. The point of zero charge (pzc) of O2-CNTs and P-CNTs were determined as function of pH. The pzc of P-CNTs and O2-CNTs are found to be 4.7 and 3.9, respectively. The adsorption data have been analyzed using Langmuir and Freundlich. Fitting the equilibrium adsorption data by Langmuir and Freundlich models shows that experimental data well explained by the Langmuir equation.
2020-05
The Theoretical Study on the Mechanism of [3+ 2] Cycloaddition Reactions between α, β-unsaturated Selenoaldehyde with Nitrone and with Nitrile Oxide
Journal of the Mexican Chemical Society (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 64)
The reaction mechanisms of [3+ 2] cycloaddition (32CA) between the α, β-unsaturated selenoaldehyde with nitrone and nitrile oxide were investigated theoretically using the molecular electron density theory (MEDT). Selenoaldehyde has two unsaturations which allow for the cycloaddition occurring. It was expected to undergo four regioisomeric reaction paths in two separate reactions with nitrone and nitrile oxide. The study was conducted using ab initio approach at MP2/6-31G (d) level of theory. Potential energy surfaces were generated from the energies of the stationary points involved in the mechanisms and the dominant reaction pathways were identified. It was found that Pathway 3 and 4 are the two competing reaction channels, where the cycloaddition reaction occurs at the selenium-analogue carbonyl group of selenoaldehyde. The reactivity indices were analysed at the ground state of the reactants to predict the reactivity of studied organic molecules in 32CA reactions. Analysis of the electronic structure of nitrone and nitrile oxide, the three-atom-components (TACs), and their participation in 32CA reactions towards selenoaldehyde allows establishing a useful classification of 32CA reactions into zwitterionin-type (zw-type) reactions involving TACs with a high zwitterionic character.
2020-04
Carbon Nanotubes for Removal of Fast Green Dye
International Research Journal of Pure and Applied Chemistry (ژمارەی وەرز (Issue) : 5) (بەرگ (Volume) : 21)
The adsorption of Fast Green (FG) dye on pristine multi-walled carbon nanotubes (CNTs) was investigated in this study. The adsorption was carried out under different operating conditions. The operating conditions were contact time, adsorbent dosage, initial dye concentration, the pH of the solution and temperature. The analysis of results found that the removal percentage of FG dye on CNTs decreases with increase in initial FG concentration. It was found that the increasing of CNTs dosage enhanced the efficiency of dye removal. It was also found that the increasing of temperature significantly enhanced the removal percent of FG dye and it is indicated that the adsorption of FG dye on CNTs was in endothermic nature. The study reports that the best pH of solution for the adsorption of FG on CNTs were 4. The adsorption data have been analyzed using Langmuir and Freundlich. Fitting the equilibrium adsorption data by Langmuir and Freundlich models shows that experimental data well explained by the Langmuir equation.
2020-04
Mechanistic study of the [2+ 2] cycloaddition reaction of cyclohexenone and its derivatives with vinyl acetate
Theoretical Chemistry Accounts (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 139)
The mechanism of [2+2] cycloaddition reaction of cyclohexenone and its derivatives with vinyl acetate was studied at the B3LYP-D3/6-311++G(d,p) level of theory. Computations showed that this reaction occurs via a stepwise mechanism. The geometries of the first and second transition states were determined. Moreover, we investigated the effect of the chalcogens of the ketone function of the cyclohexenone on the cycloaddition reactions. The activation energies decrease significantly on proceeding from oxygen (O), through sulfur (S) and onto selenium (Se). The energetic results indicate that the stability of the cycloadducts decreases on proceeding from O, through S and onto Se as confirmed by the analysis of their molecular orbitals. Moreover, we determined the pattern of the lowest singlet and triplet electronic states of these species. We proposed an explanation for the regioselectivity of these reactions for the …
2020-02

2019

Molecular Structure and Spectroscopic Studies of Some Diazo Dyes Compounds using DFT Method
2019 First International Conference of Intelligent Computing and Engineering (ICOICE)
Diazo dyes compounds have a variety biological and industrial applications. In this study, the molecular structures and the spectroscopic parameters of three synthesized diazo dyes 1–3 were computed using a Density Functional Theory DFT method with the B3LYP/6-311++G(d.p), The results indicate that all three diazo dyes are preferred thermodynamically. Compound 3 has a higher value of entropy and more negative values of heat formation and Gibb's free energy as compared to the other dyes. The FTIR spectra of 2 and 3 show that the nitro functional groups at ortho positions appear at lower symmetrical stretching frequencies. At all, there is a good agreement with the experimental results. On the other hand, the energy gap decreases in this order 2, 3 and 1, also, the FTIR spectrum of compound 1 shows a lower symmetrical stretching frequency of the nitro functional group at the para position.
2019-12
Theoretical Study of the [4+ 2] Cycloaddition Reaction of Trifluoroethylene with Five-membered Chalcogens Heterocyclic Compounds
ARO-THE SCIENTIFIC JOURNAL OF KOYA UNIVERSITY (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 7)
[4+ 2] cycloaddition reaction has enormous significant in organic chemistry synthesis reactions and yet remains unexplored for the synthesis of fluorine-containing compounds. A density functional theory study of the stereo-and regioselectivity of the [4+ 2] cycloaddition reaction of trifluoroethylene with furan, thiophene, and selenophene was carried out in the gas phase. The B3LYP functional is used throughout in combination with 6-31G (d) basis set. The analysis of stationary points and the energetic parameters indicates that the reaction mechanism is concerted and confirms that the exo-adducts are thermodynamically and kinetically more favored than endo-adducts. The calculated branching ratio indicates that the exo-adducts have the higher percent yield than endoadducts and the yield of endo-adducts is increased only slightly on proceeding from furan, through thiophene, and onto selenophene. The analysis of the frontier molecular highest occupied molecular orbital (MO) and lowest unoccupied MO orbitals indicates that the exo-adducts are more stable due to their higher energy gab. The reaction energies were compared to the MP2/6-31G (d) and CCSD (T)/6-31G (d) calculations.
2019-12
Theoretical Study for the [2+ 2] Cycloaddition Reaction Mechanism of Ketenes and their Derivatives
Oriental Journal of Chemistry (ژمارەی وەرز (Issue) : 5) (بەرگ (Volume) : 35)
This study presents the intramolecular [2+ 2] cycloaddition reaction of ketenes to form cyclobutanones using B3LYP-D3/6-311++ G (d, p) level of approximation. The concerted mechanism path was studied in detail. The structures of all intermediates and transition states were located using same level of theory. The influences of the substituents (-H,-CH3,-NH2,-F,-OH and–CN) were also discussed. The analysis of stationary points and the energetic parameters indicates that the substituted ketene with–CN group has the highest activation energy; however, ketene with–NH2 group has the lowest one. Conversely, in-tramolecular [2+ 2] cycloaddition records the highest degree of asynchronicity with–NH2 group and lowest with–CN group. The calculated thermodynamic parameters at room temperature have been listed and analyzed. The global and local properties of reactants involved in the intramolecular [2+ 2] cycloaddition reactions and the Fukui functions for an electrophilicity and local electrophilicity were also elucidated for carbon centers of each reactant.
2019-10
Electrochemical Degradation of Alizarin Black Dye in Aqueous Medium using Fe/Al Electrode
Science Journal of University of Zakho (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 7)
This work investigates the electro-catalytic degradation of alizarinblack dye in an electrochemical cell using Fe as anode and Al as cathode. The influence of initial dye concentration, effect of salt, pH, change of temperature and effect ofchange of applied voltage have been studied in addition, the influence of semiconductor dose has studied as well. In the current work roughly total removal of 70 mg/L of dye occurred in 16 minonly. The results showedthat effect of both electrolyte concentration and applied voltage was positive if combined together and the rate of degradation in neutralmedium was the best for degradation of Alizarin black dye.
2019-06

2018

Stereoselectivity and Regioselectivity of the Cycloaddition Dimerization of allyl 3-(2-pyridyl) acrylate and allyl 3-(2-pyrryl) acrylate: DFT Calculations
IOP Conference Series Materials Science and Engineering (ژمارەی وەرز (Issue) : 1) (بەرگ (Volume) : 454)
A theoretical study of the photochemical dimerization of allyl 3-(2-pyridyl) acrylate and allyl 3-(2-pyrryl) acrylate is reported. The reactions gave dimers with high regioselectivity and stereoselectivity through [2+2] cycloaddition mechanism. All calculations were computed by density functional theory method, B3LYP, in conjunction with the 6-31G(d) basis set. Conformation analysis, geometric parameters and IR spectrum for the target dimers were also studied. Conformation 2 of allyl 3-(2-pyridyl) acrylate and conformation 9 for allyl 3-(2-pyrryl) acrylate were found to be the most stable structures among the different conformations. Vibration frequencies and IR absorption intensities were calculated for the conformers 2 and 9 using the same computational method. In addition, thermodynamic parameters for the reactions of most stable conformations were analysed. The HOMO and LUMO molecular orbitals and the energy gap between them were estimated for the stable conformations.
2018-12
Photo-catalytic degradation of Toluidine Blue Dye in Aqueous Medium Under Fluorescent Light
2018 International Conference on Advanced Science and Engineering (ICOASE)
The photo-catalytic degradation of Toluidine Blue dye (TB) in aqueous suspension solution has been studied utilizing fluorescence light and using Zinc oxide (ZnO) as a semiconductor at variety working factors. The studied parameters were concentration of dye, semiconductor dose and the influence of pH. The result shows that expanding of ZnO dose from 20 to 60 mg/L increases the removal rate of TB dye. On the other hand, the adding of concentration from 5 to 15 mg/L show negative effect on the rate of photo-degradation. It has been denoted that the percentage of dye degradation come to the peak value at high acidic medium. 11 % of TB dye was adsorbed, in dark condition, by ZnO. In addition, the kinetics of degradation has been examined and the degradation was found to take after pseudo-first order kinetic model.
2018-11
Mechanism and Thermodynamic Parameters of Paternὸ-Büchi Reaction of Benzene and Furan: DFT Study
2018 International Conference on Advanced Science and Engineering (ICOASE)
The Paterno-Büchi reaction of benzene with benzaldehyde and furan with furfural were studied theoretically. The mechanism was investigated using Density Functional Theory (DFT). It was found that the final product of the benzene reaction is oxetane 3, while in the case of furan the oxetane 6 is unstable and goes through oxetane ring opening. The target of this article was to study the reaction mechanism and calculate the thermodynamic parameters of the reactions. The oxetane 3 formed was found to be stable with reaction energy of -120 kcal/mol. However, the oxetane 6 was found to be less stable with reaction energy 21 kcal/mol which tends to produce more stable product 7 through the oxetane ring opening. In addition, the molecular orbitals were calculated and analyzed for all the intermediates, oxetanes and final products.
2018-11

2017

Adsorption of Cr (Vi) Ion from Aqueous Solutions by Solid Waste of Potato Peels
Science Journal of University of Zakho (ژمارەی وەرز (Issue) : 3) (بەرگ (Volume) : 5)
Pollution of wastewater with heavy metal has always been a serious problem to the environment. Chromium is considered one of the most noxious heavy metals. Adsorption is now reorganized as an alternative technology of defence for chromium removal due to local availability, technical efficiency and cost effectiveness. Potato peel powder can be used as a low cost biosorbent to remove hexavalent chromium from aqueous solutions under various experimental conditions. Different parameters including equilibrium contact time, initial metal ion concentration, potato peel dose, pH and temperature were studied through a number of batch sorption experiments. Both the Langmuir and Freundlich were found to fit the adsorption isotherm of Cr (VI) ion onto potato peel. The Langmuir adsorption capacity was found to be 1.97 mg/g while Freundlich constants including Kf and n were 1.57 and 2.5, respectively. The adsorption kinetic was found to be more fit with the pseudo-first order model. This study showed a high efficiency of potato peel for the biosorption of Cr (VI) ion from aqueous solutions.
2017-09
Estimation and Correlation Analysis of Heavy Metals of Some Well Water in Zakho City, Iraq
Science Journal of University of Zakho (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 5)
This study was carried out to examine the concentrations of major heavy metals in fifteen different well water in Zakho City, Kurdistan Region, Iraq. The studied heavy metals were iron, copper, chromium, aluminum, cadmium, cobalt, nickel, manganese, zinc and lead. The results obtained in the studied area showed that copper, chromium, cobalt, zinc, manganese, aluminum, iron and lead were within the acceptable limits as recommended by WHO for water drinking. However, in all studied areas, cadmium and nickel were mostly founded to exceed the maximum permissible limit set by WHO. It is found that zinc and copper possess a very good positive correlation between each other. The results obtained in this study confirmed the groundwater pollution and hence it is not suitable for consumption without any prior treatment.
2017-06

2016

FENTON DEGRADATION OF FAST GREEN DYE
2nd INTERNATIONAL SCIENTIFIC CONFERENCE – UNIVERSITY OF ZAKHO (بەرگ (Volume) : 2)
The degradation of commercial textile dye named fast green (FG) was investigated by Fenton reagent under different operating conditions in an aqueous solution. The operating conditions were amount of hydrogen peroxide (0.05, 0.1 and 0.15 mL), pH (2-12) and concentration of ferrous ion (10, 20 and 30 mg). The initial rate of degradation was affected by the concentration of Fenton reagents [Fe(II) and H2O2 solution]. The rate of degradation enhanced as the concentration of ferrous ion increased. As the ferrous ion concentration increased from 10 to 30 mg, the removal percent was increased from 73% to 89%, respectively, at 25 min of reaction time. Also, the removal percent of FG increased from 74 % to 81 % as the amount of H2O2 increased from 0.05 to 0.15 mL, respectively, at 25 min of reaction time. it was also found that at pH 3 removal percent reach maximum value with 91.8%. The kinetic study of FG degradation was also studied in this work and the results indicated that the degradation kinetics of FG followed the first-order kinetic.
2016-04
Removal of Acid Alizarin Black Dye from Aqueous Solution by Adsorption Using Zinc Oxide
international Research Journal of Pure & Applied Chemistry (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 11)
The adsorption of Acid Alizarin Black (AAB) dye (C.I. 21725) on zinc oxide was investigated in this study. The adsorption was carried out under different operating conditions. The operating conditions were contact time, adsorbent dosage (10, 30, 50, 70 and 100 mg), initial dye concentration (10, 20, 30, 40, 50, 60 and 70 mg/L), the pH of the solution (2, 4, 6, 7, 8, 10 and 12) and temperature (20, 30, 40, 50 and 60°C). The removal percentage of dye on ZnO decreases from 67% to 54% with increase in initial dye concentration from 10 to 70 mg/L, respectively. It was found that the increasing of ZnO dosage enhanced the dye removal. The increasing of temperature insignificantly enhanced the removal of dye. The study reports that the best pH of solution for the adsorption of AAB on ZnO were 7 and 8. The adsorption data have been analysed using Langmuir, Freundlich and Temkin. It is indicated that the adsorption of dye onto ZnO was endothermic. The uptake process of AAB obeyed the pseudo second order kinetic expression. Removal of Acid Alizarin Black Dye from Aqueous Solution by Adsorption Using Zinc Oxide.
2016-03

2015

Photodegradation Study of Toluidine Blue Dye in Aqueous Solution using Magnesium Oxide as a Photocatalyst
International Journal of Chemistry (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 7)
The photocatalytic degradation of Toluidine Blue dye (TB) in aqueous solution was investigated under UV light in the presence of magnesium oxide (MgO) as a photocatalyst at different operating parameters. The operating conditions were photocatalyst dose, initial dye concentration and the pH of the solution. Increasing of photocatalyst dose from 10 to 70 mg enhanced the degradation rate of TB dye. However, the increasing of TB dye concentration from 2 to 8 mg/L negatively affected the degradation rate. It was found that the percent of dye removal reached the maximum value at high acidic medium. In dark condition, 15 % of dye was adsorbed by MgO. Furthermore, the kinetics involved in the degradation of TB dye was examined and the degradation was found to follow pseudo first order kinetic model.
2015-09
Photodegradation of Alizarin Black S Dye Using Zinc Oxide
Journal of Environmental Engineering and Science (ژمارەی وەرز (Issue) : 8) (بەرگ (Volume) : 4)
Zinc oxide (ZnO) has been used as heterogeneous catalyst for the degradation of Acid Alizarin Black S dye (AAB) in aqueous solutions using UV light irradiation. Experiments were conducted at various operating parameters. The operating parameters were amount of catalyst (50 mg, 100 mg and 150 mg), initial concentration of dye (30 mg/L, 50 mg/L and 70 mg/L), the pH of solution (2, 4, 6, 8, 10 and 12) and the UV light intensity (6 watt and 12 watt). The progress of the degradation reaction was monitored spectrophotometrically. It was found that the degradation process of AAB solution was accelerated with increased catalyst dosage and decreased initial concentration of AAB. It was also found that the removal efficiency of AAB significantly depend on pH value of solution. The results show that the degradation percent reaches the highest values with pH close to neutral. The data proved that removal percent of dye decreased when 6 watt lamp used instead of 12 watt lamp. The kinetic study confirmed that photocatalytic degradation of AAB dye follows a pseudo first order reaction rate.
2015-08
A comparison study of two different types of clay for heterogeneous photo degradation of dye
International Journal of Advanced and Applied Sciences (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 2)
Acid alizarin black (AAB) dye (C.I. 21725) was degraded in aqueous solution using UV light in the presence of two types of clay (C1 and C2) as a catalyst at different operating conditions. The operating conditions were concentration of catalyst dosage (10, 30 and 50 mg), initial concentration of AAB dye (10, 20 and 30 mg/L), pH (2, 4, 6, 9 and 11) and intensity of UV light (6 and 12 watt). It was found that the increasing of catalyst concentration enhanced the dye decolourisation. C1 and C2 exerted positive effects on the AAB removal whilst the initial concentration of AAB negatively affected its removal. It was also found that the removal efficiency of AAB significantly depend on pH value. In high and low pH values removal percent increase, while a reversed trend was observed at with the pH value close to neutral. The result shown that removal percent of dye increased when 12 watt lamp used instead 6 watt lamp. C1 and C2 clay were analysed by X-Ray fluorescence to determine the metal oxides in clays.
2015-02

2014

Multi-walled carbon nanotubes for heterogeneous nanocatalytic ozonation
Ozone: Science & Engineering: The Journal of the International Ozone Association (ژمارەی وەرز (Issue) : 3) (بەرگ (Volume) : 37)
Multiwalled carbon nanotubes functionalized by plasma oxygen (CNTs) have been used as heterogeneous catalysts for the ozonation of methyl orange (MO) dye (CI 13025) in aqueous solutions. It was found that the addition of CNTs significantly enhanced the dye decolorization as compared to ozone alone or when activated carbon was used at the same dose as CNTs. Both the initial ozone concentration and catalyst dosage enhanced the removal of MO. However, ozone gas concentrations higher than 6 g/m3 NTP did not further improve the decolorization rates. The removal efficiency of MO increased with pH in the range 2 to 3, while a reverse trend was observed when the pH increased from 3 to 9. The addition of a radical scavenger resulted in only a limited change in the decolorization rates suggesting that molecular ozone was the main pathway by which MO decolorization occurred in solution. However, under favorable conditions for MO attraction to CNT surface (pH = 3), the decolorization rate has significantly increased. At higher pH than the pKa value of MO (3.47) and the point of zero charge of CNT (3.87), a condition that favors the electrostatic repulsion of MO from CNT, the rates were reduced in the presence of CNT as compared to ozone alone possibly due to loss of part of the supplied ozone in un-useful parallel reactions
2014-10
Homogeneous Photocatalytic Degradation of Acid Alizarin Black Using Hydrogen Peroxide
Journal of University of Zakho (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 2)
Photocatalytic degradation of acid alizarin black (AAB) dye (C.I. 21725) in aqueous solution was investigated using UV light in the presence of hydrogen peroxide (H2O2) as a catalyst at different operating conditions. The operating conditions were concentration of catalyst dosage (0.1, 0.2 and 0.3 mL of 30 % H2O2), initial concentration of AAB dye (100, 150 and 200 mg/L) and pH (3.3, 6.84 and 10.8). It was found that the increasing of catalyst concentration enhanced the dye decolourisation. Hydrogen peroxide exerted positive effects on the AAB removal whilst the initial concentration of AAB negatively affected its removal. It was also found that the removal efficiency of AAB increased with the pH value close to neutral (pH 7), while a reversed trend was observed at acidic and basic medium.
2014-10
PHOTOCATALYTIC DEGREDATION OF ACID ALIZARIN BLACK USING POWDER AND NANOPARTICLES OF TITANIUM DIOXIDE
Journal of University of Zakho (ژمارەی وەرز (Issue) : 2) (بەرگ (Volume) : 2)
Photocatalytic degradation of acid alizarin black (AAB) dye (C.I. 21725) in aqueous solution was investigated using UV light in the presence of powder of titanium dioxide (P- TiO2) and nanoparticles of titanium dioxide (N- TiO2) as a catalyst. The operating conditions were catalyst dosage (10 and 20 mg/L) and initial concentration of AAB dye (10 and 20 mg/L). It was found that the increasing of catalyst concentration enhanced the dye decolourisation. Both catalysts exerted positive effects on the AAB removal whilst the initial concentration of AAB negatively affected its removal.
2014-06

2020

Ph.D.: Computational Investigation of the Mechanism and Regioselectivity of Some Cycloaddition Reactions
Theoretical modeling of organic synthesis is a powerful tool and leads to further insight into chemical systems. Computational chemistry allows obtaining the potential energy surface that experimentally cannot be observed, in addition to transition state calculations, which lead to better understanding the reactivity of an organic synthesis work. In the present thesis, theoretical methods will be used to examine the reaction mechanism paths, structural geometries, transition states, stereoselectivity, regioselectivity, thermodynamic parameters and Fukui functions of some cycloaddition reactions. In the thesis work by means of computational approaches, we studied certain [2+2], [4+2] and [3+2] cycloaddition reactions mainly applying density functional theory (DFT) method with different basis sets. The mechanistic aspects of the reaction paths were investigated in a concerted and stepwise fashion to predict the regioselectivity and stereoselectivity of those cycloadducts.
2020-05-05

2012

MSc: Heterogeneous Nanocatalytic Ozonation
Ozonation of methyl orange (MO) in aqueous solution was investigated using ozone in the presence and absence of multi-walled carbon nanotube (MWCNT) as a catalyst. The operating conditions were initial ozone concentrations (2-8 g/m3 NTP), initial MO concentrations (10-40 mg/L), pH (2-9), and amounts of carbon nanotubes (5-20 mg/L). Ozonation of MO in the absence of catalyst was slow. The initial ozone concentration and catalyst dosage exerted positive effects on the removal of MO by ozonation with and without MWCNTs catalyst. However, the initial MO concentration negatively affects MO removal for both systems. The maximum removal efficiency of MO was obtained with its initial concentration of 10 mg/L. The removal efficiency of MO increased with the pH value in the range of 2-3, while a reverse trend was observed when the pH increased from 3 to 9. The influence of pH value indicated that the adsorption of MO on the surface of carbon nanotubes (CNTs) was necessary for its effective degradation by CNTs catalytic ozonation. It was found that, to describe MO adsorption isotherm on CNTs surface, Langmuir isotherm was the most appropriate. The results show that the removal rate of MO was slower than without radical scavenger (sodium bicarbonate). This suggested that removal of MO proceeds through both ozonation reactions, direct and indirect. The inhibition of sodium bicarbonate on the CNTs activity at pH 7 was more significant as compared with the pH value of 3.
2012-12-12

2019

Molecular Structure and Spectroscopic Studies of Some Diazo Dyes Compounds using DFT Method
2019 First International Conference of Intelligent Computing and Engineering (ICOICE)
Diazo dyes compounds have a variety biological and industrial applications. In this study, the molecular structures and the spectroscopic parameters of three synthesized diazo dyes 1–3 were computed using a Density Functional Theory DFT method with the B3LYP/6-311++G(d.p), The results indicate that all three diazo dyes are preferred thermodynamically. Compound 3 has a higher value of entropy and more negative values of heat formation and Gibb's free energy as compared to the other dyes. The FTIR spectra of 2 and 3 show that the nitro functional groups at ortho positions appear at lower symmetrical stretching frequencies. At all, there is a good agreement with the experimental results. On the other hand, the energy gap decreases in this order 2, 3 and 1, also, the FTIR spectrum of compound 1 shows a lower symmetrical stretching frequency of the nitro functional group at the para position.
2019-12
Electrochemical Degradation of Alizarin Black Dye in Aqueous Medium Using Fe/Al Electrode
ICOASE2019
This work investigates the electro-catalytic degradation of alizarin black dye in an electrochemical cell using Fe as anode and Al as cathode. The influence of initial dye concentration, effect of salt, pH, change of temperature and effect change of applied voltage have been studied in addition, the influence of semiconductor dose has studied as well. In the current work roughly total removal of 70 mg/L of dye was 16 minute only. The results were shown that effect of both electrolyte concentration and applied voltage was positive if combined together and the rate of degradation in acidic medium was the best for degradation of Alizarin black dye.
2019-04

2018

Mechanism and Thermodynamic Parameters of Paternὸ-Büchi Reaction of Benzene and Furan: DFT Study
2018 International Conference on Advanced Science and Engineering (ICOASE)
The Paternὸ-Büchi reaction of benzene with benzaldehyde and furan with furfural were studied theoretically. The mechanism was investigated using Density Functional Theory (DFT). It was found that the final product of the benzene reaction is oxetane 3, while in the case of furan the oxetane 6 is unstable and goes through oxetane ring opening. The target of this article was to study the reaction mechanism and calculate the thermodynamic parameters of the reactions. The oxetane 3 formed was found to be stable with reaction energy of -120 kcal/mol. However, the oxetane 6 was found to be less stable with reaction energy 21 kcal/mol which tends to produce more stable product 7 through the oxetane ring opening. In addition, the molecular orbitals were calculated and analyzed for all the intermediates, oxetanes and final products.
2018-10
Stereoselectivity and Regioselectivity of the Cycloaddition Dimerization of allyl 3-(2-pyridyl) acrylate and allyl 3-(2-pyrryl) acrylate: DFT Calculations
IOP Conference Series: Materials Science and Engineering
A theoretical study of the photochemical dimerization of allyl 3-(2-pyridyl) acrylate and allyl 3-(2-pyrryl) acrylate is reported. The reactions gave dimers with high regioselectivity and stereoselectivity through [2+ 2] cycloaddition mechanism. All calculations were computed by density functional theory method, B3LYP, in conjunction with the 6-31G (d) basis set. Conformation analysis, geometric parameters and IR spectrum for the target dimers were also studied. Conformation 2 of allyl 3-(2-pyridyl) acrylate and conformation 9 for allyl 3-(2-pyrryl) acrylate were found to be the most stable structures among the different conformations. Vibration frequencies and IR absorption intensities were calculated for the conformers 2 and 9 using the same computational method. In addition, thermodynamic parameters for the reactions of most stable conformations were analysed. The HOMO and LUMO molecular orbitals and the …
2018-08

2017

Heterogeneous Photodegradation of Dye Using Two Different Types of Local Clays as a Catalysts
ICEEE2015
Photocatalytic degradation of Acid Alizarin Black S (AAB) dye (C.I. 21725) was studied, at different operating conditions, in aqueous solution using UV light in the presence of two types of local clay (B1 and B2) as a catalysts. The operating conditions were catalysts dosage (10, 30 and 50 mg), initial concentration of AAB dye (10, 20 and 30 mg/L), pH (2, 4, 6, 9 and 11) and UV light intensity (6 and 12 watt). It was found that the increasing of catalyst dosage enhanced the removal percent of dye. Clays (B1 and B2) exerted positive effects on the AAB removal whilst the initial AAB concentration negatively affected its removal. It was also found that the removal efficiency of AAB significantly depend on pH value. In high pH values removal percent increase, while a reversed trend was observed in low pH value. The result shown that removal percent of dye decreased when 6 watt lamp used instead 12 watt lamp. The data proved that B2 was more efficient than B1 for removing AAB dye. B1 and B2 clays were analysed by X-Ray fluorescence to determine the metal oxides in clays.
2017-04
FENTON DEGRADATION OF FAST GREEN DYE
2nd INTERNATIONAL SCIENTIFIC CONFERENCE – UNIVERSITY OF ZAKHO
The degradation of commercial textile dye named fast green (FG) was investigated by Fenton reagent under different operating conditions in an aqueous solution. The operating conditions were amount of hydrogen peroxide (0.05, 0.1 and 0.15 mL), pH (2-12) and concentration of ferrous ion (10, 20 and 30 mg). The initial rate of degradation was affected by the concentration of Fenton reagents [Fe(II) and H2O2 solution]. The rate of degradation enhanced as the concentration of ferrous ion increased. As the ferrous ion concentration increased from 10 to 30 mg, the removal percent was increased from 73% to 89%, respectively, at 25 min of reaction time. Also, the removal percent of FG increased from 74 % to 81 % as the amount of H2O2 increased from 0.05 to 0.15 mL, respectively, at 25 min of reaction time. it was also found that at pH 3 removal percent reach maximum value with 91.8%. The kinetic study of FG degradation was also studied in this work and the results indicated that the degradation kinetics of FG followed the first-order kinetic.
2017-04

2026

Molecular Docking in Drug Discovery
University of Zakho
Molecular docking is a computational technique used to predict how a small molecule (ligand) binds to a target protein receptor. By simulating these interactions in silico, researchers identify promising drug candidates, understand biological pathways, and optimize binding affinity before advancing to expensive, time-consuming wet-lab experiments.
2026-01

2013

EndNote X4
University of Zakho
Using EndNote for referencing in scientific articles
2013-07