The nucleophilicity N index in organic chemistry

A redefinition of global conceptual density functional theory reactivity indexes by means of the cubic expansions of the energy

In the present work, a new definition of the conceptual density functional theory reactivity indexes is proposed, based on a cubic interpolation of the energy as function of number of electrons as well as a generalization of the net electrophilicity index. This new proposal takes into account both the influence of hyperhardness on the reactivity and a weighted average of the electrodonating and electroacepting powers. Thus, the presented redefinition incorporates corrections and additional degrees of freedom to the prior CDFT indexes. Numerical support for global descriptors is presented for 30 benzhydrylium ions (i.e., charged electrophiles) and 15 alkyl and aryl nucleophiles taken as reference cases from the Mayr Database of Reactivity Parameters. In the best-case scenario, the descriptors correlated better with the electrophilicity parameter (r2 = 0.981) than with the nucleophilicity parameter (r2 = 0.827).

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

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.

Phosphate-enabled mechanochemical PFAS destruction for fluoride reuse

Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are persistent, bioaccumulative and anthropogenic pollutants that have attracted the attention of the public and private sectors because of their adverse impact on human health1. Although various technologies have been deployed to degrade PFASs with a focus on non-polymeric functionalized compounds (perfluorooctanoic acid and perfluorooctanesulfonic acid)2-4, a general PFAS destruction method coupled with fluorine recovery for upcycling is highly desirable. Here we disclose a protocol that converts multiple classes of PFAS, including the fluoroplastics polytetrafluoroethylene and polyvinylidene fluoride, into high-value fluorochemicals. To achieve this, PFASs were reacted with potassium phosphate salts under solvent-free mechanochemical conditions, a mineralization process enabling fluorine recovery as KF and K2PO3F for fluorination chemistry. The phosphate salts can be recovered for reuse, implying no detrimental impact on the phosphorus cycle. Therefore, PFASs are not only destructible but can now contribute to a sustainable circular fluorine economy.

A mechanistic insight into anionic phosphate adsorption on developed chitosan.ZnO@metakaolin biocomposite

Due to their high efficiency, chitosan (Cs)-based materials are increasingly utilized for wastewater treatment applications. In this study, a novel Cs-based biocomposite, Cs.ZnO@Mk was developed by blending Cs with zinc oxide (ZnO) and metakaolin (Mk), and was evaluated for its capability as a biosorbent to remove phosphate (PO43-) ions from water. The biosorbent was characterized using FTIR, XRD, TGA, SEM, and XPS techniques. The determined optimal conditions for PO43- removal were pH 4, initial concentration 100 mg/L, and contact time 120 min, achieving 98.9 % PO43- removal efficiency. The adsorption isotherm and kinetic data were fitted well to Langmuir isotherm and pseudo-second-order kinetic models, while thermodynamic study affirmed that the adsorption process was exothermic. XPS analysis suggested that electrostatic attraction and ligand-exchange were the key mechanisms for PO43- adsorption. Further mechanistic insights were gained through density functional theory (DFT) calculations and non-covalent interaction (NCI) analysis. Regeneration and counter-ions effect studies confirmed the effectiveness and stability of Cs.ZnO@Mk during PO43- adsorption. This demonstrates well its potential as a robust biosorbent for effective PO43- removal from industrial effluents.

Binding of a Co(III) Metalloporphyrin to Amines in Water: Influence of the pKa and Aromaticity of the Ligand, and pH-Modulated Allosteric Effect

Metalloporphyrins have been widely utilized as building blocks for molecular self-assembly in organic solvents, but their application in water is less common due to competition from water molecules for the metal center. However, Co(III) metalloporphyrins are notable for their strong binding to two aromatic amine ligands in aqueous buffers. In this study, we present a comprehensive investigation of the binding behavior of Co(III) tetraphenyl sulfonic acid porphyrin with selected aromatic and aliphatic amines in aqueous solution. Our findings reveal that the ligand affinity is influenced by the pKa values of both the ligand and the porphyrin, as well as the hybridization state of the nitrogen atom, with binding to sp3-hybridized nitrogen being significantly weaker than to sp2-hybridized nitrogen. DFT calculations further suggest that the variations in binding affinities are due to differences in the electrostatic potential at the nitrogen atoms, with aromatic ligands generally exhibiting stronger Co-N coordination due to greater electrostatic attraction. Moreover, our study and the binding model we developed demonstrate that changes in pH affect the affinity for each ligand to varying degrees, sometimes resulting in an allosteric cooperative effect. This effect is linked to electronic changes introduced by the binding of the first ligand. Our model provides a predictive tool for understanding the assembly behavior of these porphyrins in aqueous buffers, with potential applications in developing more efficient catalysts and in the creation of smart materials for fields ranging from catalysis to nanomedicine and optoelectronics.

Mechanistic Aspects of [3+2] Cycloaddition Reaction of Trifluoroacetonitrile with Diarylnitrilimines in Light of Molecular Electron Density Theory Quantum Chemical Study

In this study, we investigated the [3+2] cycloaddition reaction of CF3CN (TFAN) with nitrilimine (NI) to produce 1,2,4-triazole and compared the resulting isomers. We determined the preferred reaction pathway by examining the electrophilic and nucleophilic properties of the reaction substrates, performing thermodynamic calculations for the individual pathways, and comparing them with the experimental results.

The Investigation on the Reactivity and the Formation of Halogen Bond Complexes for the Reactions of α-Nucleophiles XO- (X = F, *Cl, Br, I) and CH3CH2Cl

Precise prediction of reactivity and accurately identifying the types of reaction complexes are prerequisites for delineating the microscopic mechanisms of ion-molecule reactions, which remain unclear for reactions involving α-nucleophilic reagents. Here, we investigate the potential energy surface of the multiatomic reactions XO- (X = F, *Cl, Br, I) + CH3CH2Cl to elucidate the optimal descriptors for reaction reactivity and the origin of halogen bond/hydrogen bond compounds. Through analyzing the orbital composition and the relationship of energy barriers with the proton affinity and nucleophilic index, the local nucleophilic index is ultimately determined to be the optimal descriptor for predicting the reactivity of the reactions with α-nucleophilic reagents. Furthermore, it is found that the type of a reaction complex is closely related to the initial relative orientations of ions and molecules, the functional group substitutions, and the electrostatic potential extreme points of the halogen tops in the reactive substrates. In terms of the above factors, we can design suitable reaction substrates to generate intermolecular interactions with specific types, which is important in areas such as drug synthesis.

Quantum DFT analysis and molecular docking investigation of various potential breast cancer drugs

Breast cancer is among the deadliest cancers worldwide, highlighting the urgent need for effective treatments. This study employs density functional theory (DFT) and molecular docking analyses to evaluate the anti-cancer efficacy and specificity of drug molecules lapatinib, tucatinib, neratinib, anastrozole, and letrozole. DFT analysis provides comprehensive insights into the structural, electronic, optical, and vibrational properties of these drugs, helping to elucidate their molecular stability and reactivity through global reactivity descriptors. Additionally, molecular docking simulations reveal the binding conformations and interaction profiles of these drugs with key breast cancer targets, underscoring their therapeutic potential. Docking results indicate that lapatinib, tucatinib, and neratinib have high binding affinities for HER2, with lapatinib exhibiting the strongest overall binding, particularly with PDK1 (PDB ID: 1UU7), PAK4 (PDB ID: 2X4Z), GSK3 (PDB ID: 1GNG), and HER2 (PDB ID: 2IOK). The stable hydrogen bonding and other interactions observed with lapatinib support its effectiveness in treating HER2-positive breast cancers, tucatinib's selective HER2 binding reduces off-target effects, while neratinib's irreversible binding provides prolonged inhibition, making it useful for overcoming resistance in HER2-positive cases. In contrast, anastrozole and letrozole show lower binding affinities for HER2 and EGFR due to their simpler structures but are potent aromatase inhibitors, making them effective in treating estrogen receptor-positive (ER-positive) breast cancers. In conclusion, DFT and molecular docking studies affirm the suitability of lapatinib, tucatinib, and neratinib for HER2-positive cancers, while anastrozole and letrozole are effective in ER-positive cancers, emphasizing the role of molecular structure and binding affinity in optimizing cancer treatment strategies.

π-π stacking assisted regioselectivity regulation in palladium-catalyzed cyclization reactions: a theoretical study

The regulation of regioselectivity is an objective often pursued by organic chemists, and the comprehension of its mechanisms is crucial for devising efficient synthetic pathways. In this report, we conducted theoretical calculations to explore the regioselectivity regulatory mechanisms of two palladium-catalyzed cyclization reactions. In these cyclization reactions, manipulating the structural differences in the reaction substrates leads to the formation of distinct products. A detailed reaction mechanism and reactivity profile for this reaction were revealed. Furthermore, a π-π stacking assisted regioselectivity regulatory mechanism was proven by distortion-interaction energy analysis and noncovalent interaction calculations. The calculated results presented herein provide a theoretical guide for further experimental investigations of regioselectivity regulation.

DFT rationalization of the mechanism and selectivity in a gold-catalyzed oxidative cyclization of diynones with alcohols

The mechanism, regioselectivity, and chemoselectivity in a gold-catalyzed oxidative cyclization of diynones with alcohols to give furan-3-carboxylate derivatives were explored by density functional theory (DFT). The obtained results revealed that the first step of the global reaction involves a nucleophilic attack of a pyridine-N-oxide derivative on the catalyst-ligated diynone, forming a vinyl intermediate that can isomerize to an α,α'-dioxo gold carbene upon the cleavage of the N-O bond. In the second step, a nucleophilic addition is also completed via pyridine-N-oxide instead of an alcohol proposed in the experiment. In the following steps, the selective nucleophilic addition of alcohol, 1,2-alkynyl migration, five-membered cyclization, and protodeauration lead to the furan-based products with the regeneration of the gold catalyst. The unique features of regio- and chemoselectivity were investigated in detail by the global reactivity index (GRI) and distortion/interaction analyses. Apart from fully rationalizing the experimental data, the DFT results provide an important contribution to understanding, optimizing, and further developing the related types of organic transformations.

DFT investigation of the mechanism and role of N-heterocyclic carbene (NHC) in constructing asymmetric organosilanes using NHC-catalyzed [4+2] cycloaddition reaction

Herein, the mechanism and origin of stereoselectivity for the asymmetric [4+2] cycloaddition between (E)-3-(p-tolyl)acrylaldehyde (R1) and phenyl-3-(trimethylsilyl)prop-2-en-1-one (R2) in the presence of an N-heterocyclic carbene (NHC) were theoretically scrutinized. The desirable catalytic cycle is characterized by five steps: (1) the coupling reaction of the NHC catalyst with R1, the formation of the Breslow and enolate intermediates in the second and third steps, (4) the formal [4+2] cycloaddition reaction to form the stereoselective C-C bond, and (5) the regeneration of NHC to obtain asymmetric organosilanes. In the most energetically favorable pathway, the formation of the enolate intermediate exhibits the highest energy barrier of about 19.48 kcal mol-1 (Re-TS2BA) and is the rate-determining step. The [4+2] cycloaddition reaction is the stereoselectivity-determining step forming the chiral C-C bond with RR, RS, SR and SS configurations, among which RS is the most desirable configuration. The origin of stereoselectivity was investigated using distortion energy analysis. The first and fourth steps helped in investigating the effects of electron-donating (Me) and electron-withdrawing (Cl) groups on cinnamaldehyde. Conceptual DFT (CDFT) analysis was carried out to confirm the critical role of the NHC catalyst as a Lewis base during the reaction processes.

Metabolite identification of emerging disinfection byproduct dibromo-benzoquinone in vivo and in vitro: Multi-strategy mass-spectrometry annotation and toxicity characterization

Halobenzoquinones (HBQs) are emerging disinfection byproducts (DBPs) of high toxicity and also are shared active toxic intermediates of multiple halogenated organic pollutants. Due to the strong oxidizing property and electrophilicity, HBQs exhibit extremely diverse metabolism pathways in organisms. The identification of toxic-decisive metabolites is pivotal, albeit challenging, for understanding the toxicity mechanisms of HBQs. We employed dibromo-benzoquinone (DBBQ) as a representative HBQ, and established a systematic analytical strategy using high-resolution mass spectrometry, which collectively coupled suspect screening (SS), mass defect filtering (MDF), product ion filtering (PIF), isotopic signature filtering (ISF), and molecular networking (MN). As a result, 20 biotransformation products of DBBQ were identified in vivo and in vitro, involving metabolism reactions such as hydroxylation, methylation, methoxylation, acetylation, sulfonation, glucuronidation, glutathionylation, dimerization, and conjugation with amino acids or fatty acids. Quantitative structure-activity relationship (QSAR) analysis and cytotoxicity experiments consistently demonstrated the significantly high toxicity of the fatty acid conjugate compared to the parent compound DBBQ and other metabolites, pinpointing the important role of the fatty acid conjugation in determining the metabolism and toxicity of HBQs. The research conducted a comprehensive evaluation of the metabolism of a typical HBQ with the combination of multiple analytical and toxicity characterization methods, therefore screen out the most important metabolism pathway of HBQs.

Insights into the mechanism, selectivity, and substituent effects in the Diels-Alder reaction of azatrienes with electron-rich dienophiles: An MEDT study

The reactivity and mechanistic intricacies of azatrienes in Diels-Alder reactions have been relatively unexplored despite their intriguing potential applications. In this study, we employ Molecular Electron Density Theory to theoretically investigate the hetero-Diels-Alder reaction involving azatrienes with ethyl vinyl ether and allenyl methyl ether. Analysis of Conceptual Density Functional Theory, energetic profiles, and the topological characteristics is conducted to elucidate the reactions. The revealed mechanism manifests as a polar one-step two-stages process under kinetic control. We establish a clear relationship of between the periselectivity, regioselectivity, and stereoselectivity on one hand and the characteristics of the reactions mechanism on the other hand. The influence of weak interactions on reaction activation barriers and bonding evolution are discussed in detail. We demonstrate that substituents enhancing the reverse electron density flux facilitate the feasibility of the reactions. The results lay ground for a meticulous control of the reaction of azatriene in similar synthetic scenarios.

Unexpected Course of Reaction Between (1E,3E)-1,4-Dinitro-1,3-butadiene and N-Methyl Azomethine Ylide-A Comprehensive Experimental and Quantum-Chemical Study

In recent times, interest in the chemistry of conjugated nitrodienes is still significantly increasing. In particular, the application of these compounds as building blocks to obtain heterocycles is a popular object of research. Therefore, in continuation of our research devoted to the topic of conjugated nitrodienes, experimental and quantum-chemical studies of a cycloaddition reaction between (1E,3E)-1,4-dinitro-1,3-butadiene and N-methyl azomethine ylide have been investigated. The computational results present that the tested reaction is realized through a pdr-type polar mechanism. In turn, the experimental study shows that in a course of this cycloaddition, only one reaction product in the form of 1-methyl-3-(trans-2-nitrovinyl)-Δ3-pyrroline is created. The constitution of this compound has been confirmed via spectroscopic methods. Finally, ADME analysis indicated that the synthesized Δ3-pyrroline exhibits biological potential, and it is a good drug candidate according to Lipinski, Veber and Egan rules. Nevertheless, PASS simulation showed that the compound exhibits weak antimicrobial, inhibitory and antagonist properties. Preliminary in silico research shows that although the obtained Δ3-pyrroline is not a good candidate for a drug, the presence of a nitrovinyl moiety in its structure indicates that the compound is an initial basis for further modifications.

Alanazi M, Nemes G, El. Yazidi M. New Quinazolin-4(3H)-One Derivatives Incorporating Isoxazole Moiety as Antioxidant Agents: Synthesis, Structural Characterization, and Theoretical DFT Mechanistic Study

Background: This research centers on the development and spectroscopic characterization of new quinazolin-4(3H)-one-isoxazole derivatives (5a-e). The aim was to investigate the regioselectivity of the 1,3-dipolar cycloaddition involving arylnitriloxides and N-propargylquinazolin-4(3H)-one, and to assess the antioxidant properties of the synthesized compounds. The synthetic approach started with the alkylation of quinazolin-4(3H)-one using propargyl bromide, followed by a 1,3-dipolar cycloaddition reaction. Methods: The structural identification of the products was performed using various spectroscopic methods, such as IR, 1H, 13C, and HMBC NMR, HRMS, and single-crystal X-ray diffraction. To further examine the regioselectivity of the cycloaddition, Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d) level were employed. Additionally, the antioxidant potential of the compounds was tested in vitro using DPPH (2,2-Diphenyl-1-picrylhydrazyl)radical scavenging assays. The reaction selectively produced 3,5-disubstituted isoxazoles, with the regiochemical outcome being independent of the substituents on the phenyl ring. Results: Theoretical calculations using DFT were in agreement with the experimental results, revealing activation energies of -81.15 kcal/mol for P-1 and -77.32 kcal/mol for P-2, favoring the formation of P-1. An analysis of the Intrinsic Reaction Coordinate (IRC) confirmed that the reaction proceeded via a concerted but asynchronous mechanism. The antioxidant tests demonstrated that the synthesized compounds exhibited significant radical scavenging activity, as shown in the DPPH assay. The 1,3-dipolar cycloaddition of arylnitriloxides with N-propargylquinazolin-4(3H)-one successfully resulted in novel 3,5-disubstituted isoxazoles. Conclusions: The experimental findings were well-supported by theoretical predictions, and the antioxidant assays revealed strong activity, indicating the potential for future biological applications of these compounds.

From farm to pharma: Investigation of the therapeutic potential of the dietary plants Apium graveolens L., Coriandrum sativum, and Mentha longifolia, as AhR modulators for Immunotherapy

Autoimmune diseases represent a complex array of conditions where the body's immune system mistakenly attacks its own tissues. These disorders, affecting millions worldwide, encompass a broad spectrum of conditions ranging from rheumatoid arthritis and multiple sclerosis to lupus and type 1 diabetes. The Aryl hydrocarbon receptor (AhR) translocator, expressed across immune and other cell types, plays crucial roles in immune disorders and inflammatory diseases. With a realm towards natural remedies in modern medicine for disease prevention, this study investigates the electronic properties and behaviors of bioactive compounds from dietary sources, including Apium graveolens L. (Celery), Coriandrum sativum seeds (Coriander), and Mentha longifolia, as AhR modulators. Through comprehensive analysis (HOMO-LUMO, ESP, LOL, and ELF), electron-rich and -poor regions, electron localization, and delocalization are identified, contrasting these compounds with the toxic AhR ligand, TCDD. Evaluation of Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties reveals favorable pharmacokinetics without blood-brain barrier penetration, indicating drug-like characteristics. Molecular docking demonstrates stronger interactions of dietary flavonoid ligands with AhR transcription compared to TCDD. Molecular dynamics simulations confirm the stability of complexes and the sustainability of interactions formed. This research underscores the potential of natural compounds as effective AhR modulators for therapeutic interventions in immune-related disorders.

Accessing the Cloke-Wilson Rearrangement via Conjugate Addition of Phosphoranes to Michael Acceptors: A Route to Cyclopropanes and 5-Membered Ring Heterocycles Investigated by Density Functional and Ab Initio Theory

Conjugate addition of unstabilized Wittig-type phosphonium ylides to 1,1-diacceptor- and 1-acceptor-substituted alkenes is investigated by density functional theory and high-level ab initio (DLPNO-CCSD(T)) calculations. The results indicate that the initial conjugate addition step should be facile with barriers predicted to be between 0 and 21 kcal mol-1. Potential intramolecular follow-up reactions include the formation of acceptor-substituted cyclopropanes as well as the formation of dihydrofuran derivatives via intramolecular SN2-type transition state structures. The barriers calculated for these potentially valuable cyclization reactions are substantial with Gibbs free energies of activation between 19 and 40 kcal mol-1. Competing reaction channels include Wittig olefination (for ketones and aldehydes), as well as Claisen condensation reactions. The reaction offers an alternative entry point to the nucleophile-catalyzed Cloke-Wilson rearrangement.

Phthalazine as a Diene in Diels-Alder Reactions With P- and As-Containing Anionic Dienophiles: Comparison of Possible Reaction Channels

Phthalazine can behave as a diene in Diels-Alder (DA) cycloadditions, typically at the pyridazine ring, however, its application is somewhat limited because these reactions usually require harsh conditions or sophisticated catalysts. As an unconventional example, phthalazine was reported to undergo cycloaddition with the [PCO]- anion without any catalyst. In this computational study, we scrutinise the mechanism of the DA reactions between phthalazine and the so far known [ECX]- (E: P, As; X: O, S, Se) anions as dienophiles. In principle, the attack of an [ECX]- anion may occur at two different sites of phthalazine, either at the benzene or the pyridazine ring, and both of these possible reaction channels were juxtaposed on the basis of energetic aspects. In all of the investigated cases, the analysis of the energy profiles reveals a clear regioselectivity that favours the attack at the pyridazine ring. As a result, so far unprecedented 2-pnictanaphth-3-olate analogues seem achievable as final products. Comparing the characteristics of these pathways allowed us to clarify the source of this regioselectivity: The pyridazine ring of phthalazine exhibits lower aromaticity than the benzene subring; therefore, in the DA step, the former ring shows a higher affinity toward a dienophile than the latter, leading to lower activation barriers. To further map the electronic and structural features of the cycloaddition steps, the local interactions evolving in the transition states were analysed and compared using global and local descriptors. In most aspects, the characteristics of both pathways were found to be rather similar, in contrast to the markedly differing activation barriers on the two routes.

Charge transfer interaction revisited by a Fermi-Dirac derived approach

CONTEXT

In this article, we adapt a recent proposition to use a Fermi-Dirac-type population scheme on Kohn-Sham molecular orbitals to the case of an interaction with a thermalised electrode. This allows to derive a fundamental non-linear equation linking the chemical potential of the electrode and the amount of charge transferred to the system under study, hence allows to quantify the propensity to charge transfer (philicity). This methodology is applied to a large set of common electrophiles and nucleophiles, showing decent relation with more standard philicity descriptors. Chemical hardness is also revisited by this approach.

METHODS

All calculations were performed using the Gaussian 16 software package at the M062X/aug-cc-pvtz level of theory. Data analysis was then performed through a Python3 dedicated program (relying on the fsolve numerical solver from the SciPy package), using Gaussian output files, and available as supplementary material.

Computational discovery of dual potential inhibitors of SARS-CoV-2 spike/ACE2 and Mpro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics

To find drugs against COVID-19, caused by the SARS-CoV-2, promising targets include the fusion of the viral spike with the human angiotensin-converting enzyme 2 (ACE2) as well as the main protease (Mpro). These proteins are responsible for viral entry and replication, respectively. We combined several state-of-the-art computational methods, including, protein-ligand interaction fingerprint, 3D-pharmacophores, molecular-docking, MM-GBSA, DFT, and MD simulations to explore two databases: ChEMBL and NANPDB to identify molecules that could both block spike/ACE2 fusion and inhibit Mpro. A total of 1,690,649 compounds from the two databases were screened using the pharmacophore model obtained from PLIF analysis. Five recent complexes of Mpro co-crystallized with different ligands were used to generate the pharmacophore model, allowing 4,829 compounds that passed this prefilter. These were then submitted to molecular docking against Mpro. The 5% top-ranked docking hits from docking result having scores < -8.32 kcal mol-1 were selected and then docked against spike/ACE2. Only four compounds: ChEMBL244958, ChEMBL266531, ChEMBL3680003, and 1-methoxy-3-indolymethyl glucosinolate (4) displayed binding energies < - 8.21 kcal mol-1 (for the native ligand) were considered as putative dual-target inhibitors. Furthermore, predictive ADMET, MM-GBSA and DFT/6-311G(d,p) were performed on these compounds and compared with those of well-known antivirals. DFT calculations showed that ChEMBL244958 and compound 4 had significant predicted reactivity values. Molecular dynamics simulations of the docked complexes were run for 100 ns and used to validate the stability docked poses and to confirm that these hits are putative dual binders of the spike/ACE2 and the Mpro.

Chromone-isoxazole hybrids molecules: synthesis, spectroscopic, MEDT, ELF, antibacterial, ADME-Tox, molecular docking and MD simulation investigations

A mechanistic study was performed within the molecular electron density theory at the B3LYP/6-311G (d,p) computational level to explain the regioselectivity observed. An electron localization function analysis was also performed, and the results confirm the zwitterionic-type (zw-type) mechanism of the cycloaddition reactions between nitrile oxide and alkylated 4H-chromene-2-carboxylate derivatives and shed more light on the obtained regioselectivity experimentally. In silico studies on the pharmacokinetics, ADME and toxicity tests of the compounds were also performed, and it was projected that compounds 5a, 5b, 5c and 5d are pharmacokinetic and have favorable ADME profiles. Moreover, docking and molecular dynamics investigations were conducted to evaluate the interactions, orientation and conformation of the target compounds on the active sites of four distinct enzymes. The results of this investigation showed that two compounds, 5a and 5c, interacted effectively with the S. aureus active site while maintaining acceptable binding energy.Communicated by Ramaswamy H. Sarma.

Virtual screening, molecular dynamics and density functional theory on pain inhibitors against TRPV1 associating inflammatory conditions

Transient receptor potential vanilloid 1 protein (TRPV1) is expressed widely in skin and sensory neurons that contribute to pain/heat sensation in the human system. TRPV1 gene polymorphisms are susceptible to multiple diseases and it is considered a therapeutic target for various inflammatory conditions. Among the TRPV1 variants, rs8065080 (1911 A > G) plays a vital role in painful osteoarthritis and migraine. The presence of rs8065080 polymorphism may render drug efficacy. This study aimed to identify better antagonists against wild-type and variant TRPV1 that may help in the relief of pain/inflammation. We constructed suitable TRPV1 protein structures for wild-type and rs8065080 variant through a homology modelling approach. A total of 3363 anti-inflammatory compounds with high chemical diversity and good drug-like properties were collected and screened against the generated structures. Molecular docking showed that nobilamide B had the highest binding affinity (-5.83 kcal/mol) towards the wild-type. Whereas, isoquinoline analogue displayed highest binding potency with the variant TRPV1 (-11.65 kcal/mol). Besides those, C18H15F3N4O showed affinity towards both wild-type (-5.53 kcal/mol) and variant TRPV1 (-9.75 kcal/mol). Then, molecular dynamic simulation revealed stable conformation in wild-type and variant TRPV1 upon binding of nobilmaide B, isoquinoline analogue and C18H15F3N4O. Additionally, density functional theory (DFT) using B3LYP hybrid function showed high chemical reactiveness of nobilamie B, isoquinoline analogue and C18H15F3N4O. Overall, our systematic investigations provide, C18H15F3N4O could be a potential analgesic inhibiting both wild-type and variant TRPV1 against inflammatory conditions.

MEDT analysis of mechanism and selectivities in non-catalyzed and lewis acid-catalyzed diels-alder reactions between R-carvone and isoprene

Within the context of Molecular Electronic Density Theory (MEDT), this study investigates the Diels-Alder reaction among isoprene (2) and R-carvone (1R) applying DFT simulations, with and without Lewis acid (LA) catalysis. The results show that carvone (1R) acts as an electrophile and isoprene (2) as a nucleophile in a polar process. LA catalysis increases the electrophilicity of carvone, thereby improving the reactivity and selectivity of the reaction by reducing the activation Gibbs free energy. Parr functions reveal that the C5=C6 double bond is more reactive than the C9=C10 double bond, indicating chemoselectivity. The examination of the Electron Localization Function (ELF) reveals high regio- and stereoselectivity, indicating an asynchronous mechanism for the LA-catalyzed DA reaction. Furthermore, it is suggested that cycloadduct 3 has great anti-HIV potential because it exhibits lower binding energies than azidothymidine (AZT) in the docking studies of cycloadducts 3 and 4 amongst a primary HIV-1protein (1A8O plus 5W4Q).

Theoretical insights into enantioselective [2 + 1] cyclopropanation reactions of diazo compounds with electron-deficient olefins

CONTEXT

The cyclopropane skeleton plays a significant role in bioactive  molecules due to its distinctive structural properties. This has sparked keen interest and in-depth exploration in the field of stereoselective synthesis of cyclopropane derivatives. In the present study, the mechanism and the origin of stereoselectivity of diastereodivergent synthesis of cyclopropane derivatives via the catalyst-free [2 + 1]-cyclopropanation reactions of 3-diazo-N-methylindole (R1) with two types of electron-deficient olefins (R2 and R3) in both aqueous and toluene media have been studied using the DFT calculations. The findings indicate that these [2 + 1] cycloaddition reactions proceed in two stages, where the first step is not only the rate-determining step but also critically dictates the stereoselectivity of the product. The calculated diastereomeric ratios are in agreement with the experimental results. Furthermore, by utilizing non-covalent interaction (NCI) analysis and energy decomposition analysis based on molecular force fields (EDA-FF), we elucidated that the electrostatic interactions between reactant fragments in the transition state TS1s for the first step are the predominant factors determining the stereoselectivity, as opposed to the experimentally hypothesized steric hindrance and π-π stacking interactions.

METHODS

The geometrical structures of all minima and transition states on the potential energy surface (PES) in solvents water and toluene were fully optimized using the DFT method at the M06-2X(D3)/SMD/6-31 + G(d,p) level of theory. Single-point energy calculations were carried out based on the optimized geometries in the solution at the M06-2X(D3)/6-311 + G(d,p) level. All the DFT calculations were performed using the Gaussian 09 software. The optimized molecular structures were visualized using CYLview software. NCI analysis was performed using the Multiwfn and VMD softwares. The Multiwfn program was also used for CDFT and EDA-FF analyses.

Mechanistic Insights into Oxidation of Benzaldehyde by Co-Peroxo Complexes

Transition metal-peroxide complexes play a crucial role as intermediates in oxidation reactions. To unravel the mechanism of benzaldehyde oxidation by the Co-peroxo complex, we conducted density functional theory (DFT) calculations. The identified competing mechanisms include nucleophilic attack and hydrogen atom transfer (HAT). The nucleophilic attack pathway involves Co-O cleavage and nucleophilic attack, leading to the formation of the benzoate product. And the HAT pathway comprises O-O cleavage and HAT, ultimately resulting in the benzoate product. DFT calculations revealed that the formation of the end-on Co-superoxo complex 2 through Co-O cleavage, starting from the side-on Co-peroxo complex 1, is much more favorable than the formation of the two-terminal oxyl-radical intermediate 3 through O-O cleavage. Compared with the nucleophilic attack of benzaldehyde by 2, the abstraction of a hydrogen atom from benzaldehyde by 3 requires higher energy. The nature of the nucleophilicity of 2 and 3 accounts for the reactivity of the reaction.

A simple synthesis of α-Costic acid analogue with antibacterial potential, DFT and molecular docking

Natural products extracted from plants has been recognized as the most efficient starting materials to synthesize new derivatives of medicinal interest. Our research focuses on the isolation and characterization of sesquiterpene derivatives from Dittrichia Viscosa (L), as well as their hemisynthesis. To that end, a phytochemical study of Dittrichia viscosa leaves was conducted in order to obtain a sesquiterpenoid, α -Costic acid, which will be further transformed to γ -Costic acid with high yield using simple processes. Optimized molecular geometry and vibrational frequencies of both products were computed using the density functional theory. In addition, the antibacterial activity of isolated and hemisynthesized products were analyzed in vitro against Escherichia coli resistant to β-lactamase 616, Pseudomonas aeruginosa, and Staphylococcus aureus. The obtained compounds were investigated by in silico biological method to evaluate their potential inhibitory activity against same strains using FtsA, LasR proteins and DNA polymerase III enzyme.

Synthesis of eugenol derivative by the ring opening of epoxide eugenol and its analysis through chemical reactivity: a DFT approach

Eugenol, a plant bioactive component, is frequently found in a variety of medicinal plants with well-defined functional attributes. Essential oils containing eugenol were extracted from buds of Eugenia caryophyllata commonly named clove using hydrodistillation. Afterwards, the analysis of the essential oils using gas chromatography/mass spectrometry (GC/MS) shows that eugenol is the major constituent with 70.14% of it. The alkene group in eugenol was epoxidised using m-chloroperbenzoic acid leading to the synthesis of epoxide eugenol. The epoxide ring was cleaved to vanillyl glycol by mixed the epoxide eugenol with aluminum chloride hydrate in an ethanolic medium. A Density Functional Theory (DFT) study was investigated to understand the reactivity of the epoxide eugenol with the aluminum chloride hydrate. The results obtained from DFT based reactivity descriptors were in good agreement with the experiment results.

3D-QSAR, molecular docking, simulation dynamic and ADMET studies on new quinolines derivatives against colorectal carcinoma activity

Cancer is the uncontrolled spread of abnormal cells that results in abnormal tissue growth in the affected organ. One of the most important organs is exposed to the growth of colon cancer cells, which start in the large intestine (colon) or the rectum. Several therapeutic protocols were used to treat different kinds of cancer. Recently, several studies have targeted tubulin and microtubules due to their remarkable prefoliation. Also, recent research shows that quinoline compounds have significant efficacy against human colorectal cancer. So, the present work investigated the potential of thirty quinoline compounds as tubulin inhibitors using computational methods. A 3D-QSAR approach using two contours (CoMFA and CoMSIA), molecular docking simulation to determine the binding type of the complexes (ligand-receptor), molecular dynamics simulation and identifying pharmacokinetic characteristics were used to design molecules. For all compounds designed (T1-5), molecular docking was used to compare the stability by type of binding. The ADMET has been utilized for molecules with good stability in molecular docking (T1-3); these compounds have good medicinal characteristics. Furthermore, a molecular dynamics simulation (MD) at 100 ns was performed to confirm the stability of the T1-3 compounds; the molecules (T1-3) remained the most stable throughout the simulation. The compounds T1, T2 and T3 are the best-designed drugs for colorectal carcinoma treatments.Communicated by Ramaswamy H. Sarma.

Comparative investigation of derivatives of (E)-N-((E)-3-phenylallylidene)aniline: Synthesis, structural characterization, biological evaluation, density functional theory analysis, and in silico molecular docking

Bacterial resistance to antibiotics poses a significant global challenge for the public sector. Globally, researchers are actively investigating solutions to tackle the issue of bacterial resistance to antibiotics, with Schiff bases standing out as promising contenders in the fight against antimicrobial resistance. This study focused on synthesizing a series of Schiff bases (CA1-CA10) by reacting cinnamaldehyde with various aniline derivatives. Various analytical techniques, such as NMR, FTIR, UV-Vis, elemental analysis, and mass spectrometry, were employed to elucidate the structures of the synthesized compounds. Furthermore, crystal structure of CA8 was obtained using single crystal X-ray spectroscopy. The compounds were subjected to in vitro testing to assess their antibacterial and antifungal properties against eleven bacterial strains and four fungal strains. The results revealed diverse activity levels against the pathogens at varying concentrations, with notable potency observed in compounds CA3, CA4, CA9, and CA10, as indicated by their minimum inhibitory concentrations (MIC) values. The observed activity of the compounds seemed to be influenced by the specific substituents attached to their molecular structure. By conducting computational and molecular docking studies, the electronic properties of the compounds were investigated, further substantiating their potential as effective antimicrobial agents.

Insights into the mechanism of [3+2] cycloaddition reactions between N-benzyl fluoro nitrone and maleimides, its selectivity and solvent effects

We present a theoretical study of the [3+2] cycloaddition (32CA) reactions of N-benzyl fluoro nitrone with a series of maleimides producing isoxazolidines. We use the Molecular Electron Density Theory at the MPWB1K/6-311G(d) level. We focus on the reaction mechanism, selectivity, solvent, and temperature effects. In addition, we perform topological analyses at the minimal and transition states to identify the intermolecular interactions. Electron Localization Function approach classifies the N-benzyl fluoro nitrone as zwitterionic (zw-) three-atom components (TACs), associated with a high energy barrier. The low polar character of the reaction is evaluated using the Conceptual Density Functional Theory analysis of the reactants, confirmed by the low global electron density transfer computed at the transition states. Computations show that these 32CA reactions follow a one-step mechanism under kinetic control, with highly asynchronous bond formation and no new covalent bond is formed at the TS. Besides, the potential energy surfaces along the reaction pathways in gas phase and in solvent are mapped. The corresponding Gibbs free energy profiles reveal that the exo-cycloadducts are kinetically and thermodynamically more favored than endo-cycloadducts, in agreement with the exo-selectivity observed experimentally. In particular, we found that solvent and temperature did not affect this selectivity and mainly influence the activation energies and the exothermic character of these 32CA reactions.

(1E,3E)-1,4-Dinitro-1,3-butadiene-Synthesis, Spectral Characteristics and Computational Study Based on MEDT, ADME and PASS Simulation

The chemistry of conjugated nitrodienes is becoming increasingly popular. These molecules are successfully applied in cycloaddition to synthesize six-membered rings in Diels-Alder reactions. Nitrodienes can be also applied to obtain bis-compounds in [3+2] cycloaddition. Moreover, the presence of a nitro group in the structure provides a possibility of further modification of the products. The simplest symmetrical representative of conjugated nitrodienes is (1E,3E)-1,4-dinitro-1,3-butadiene. Although the first mentions of the compound date back to the early 1950s, the compound has not yet been examined thoroughly enough. Therefore, in this article, a comprehensive study of (1E,3E)-1,4-dinitro-1,3-butadiene has been described. For this purpose, an experimental study including the synthesis process as well as an evaluation of the spectral characteristics has been conducted. So as to better understand the properties of this compound, a computational study of reactivity indices based on MEDT and also an assessment of pharmacokinetics and biological activity according to ADME and PASS methodologies have been made. On this basis, some future application trends of (1E,3E)-1,4-dinitro-1,3-butadiene have been proposed.

New Cap-Holed AlP, GaP, and InP Nanotubes

The structural, vibrational, and electronic properties of new inorganic X-phosphide nanotubes (ch-XPNT), with X = Al, Ga, or In and chirality of (5,5), are investigated. These new NTs display cap-hole ends, with the cap-hole features induced by the nonpassivated ends. Studies are based on density functional theory (DFT) using the M06-2X, PBE, and B3LYP functionals together with the LanL2DZ basis set. All nanostructures have been relaxed by minimizing the total energy, assuming a nonmagnetic nature and a total neutral charge. Note that the cap-hole NTs are terminated by a 10-atom ring, which in turn favors the geometrical ordering and yields stable structures. The (5,5) ch-XPNT are highly electrophilic and nonpolar, in addition to having high solvation energy values. Let us remark that solvation energies are produced by the intermolecular forces that involve the induced dipoles. Structural and vibrational results show that the X-P bonds are single bonds. Finally, results suggest that the inorganic nanotubes are structurally stable with semiconductor features, which means that their functionalization may yield interesting future applications.

DFT Exploration of Metal Ion-Ligand Binding: Toward Rational Design of Chelating Agent in Semiconductor Manufacturing

Chelating agents are commonly employed in microelectronic processes to prevent metal ion contamination. The ligand fragments of a chelating agent largely determine its binding strength to metal ions. Identification of ligands with suitable characteristics will facilitate the design of chelating agents to enhance the capture and removal of metal ions from the substrate in microelectronic processes. This study employed quantum chemical calculations to simulate the binding process between eleven ligands and the hydrated forms of Ni2+, Cu2+, Al3+, and Fe3+ ions. The binding strength between the metal ions and ligands was quantified using binding energy and binding enthalpy. Additionally, we explored the binding interaction mechanisms and explained the differences in binding abilities of the eleven ligands using frontier molecular orbitals, nucleophilic indexes, electrostatic potentials, and energy decomposition calculations based on molecular force fields. Based on our computational results, promising chelating agent structures are proposed, aiming to guide the design of new chelating agents to address metal ion contamination issues in integrated circuit processes.

Combined FTIR/Raman spectroscopic studies and ab initio electronic structure calculations of Dithiothreitol

A total of seven minimum energy geometries were obtained on exploring the conformational landscape of dithiothreitol (DTT) by varying the prominent dihedral angles in the molecule through a relaxed scan with a step size of 5° at B3LYP/cc-pVTZ with further geometry optimization at CCSD/cc-pVDZ level of theory. Single point energies were calculated for all the conformers at CCSD(T)/CBS limit with cc-pVNZ (N = T, Q) level of theory and revealed the similar energy pattern. The two conformers, namely G'TG'1 and G'TT, were found iso-energic even though they differed in their structure significantly and were of the lowest energy compared to others. Energies corresponding to the cyclic as well as other configurational counterpart of the global minimum were found much higher in energy compared to the global minimum structure. Intramolecular sulfur centered hydrogen bond was seen to stabilize the global minimum structure of DTT as revealed by AIM, NBO, FMO and ESP charge analysis. Computed NMR of DTT matched well with the experimental data gleaned from the literature. Vibrational spectra (Raman and IR) were measured and compared with computed normal modes of DTT, which were found in good agreement.

Marine Toxins as Pharmaceutical Treasure Troves: A Focus on Saxitoxin Derivatives from a Computational Point of View

This work highlights the significant potential of marine toxins, particularly saxitoxin (STX) and its derivatives, in the exploration of novel pharmaceuticals. These toxins, produced by aquatic microorganisms and collected by bivalve mollusks and other filter-feeding organisms, offer a vast reservoir of chemical and biological diversity. They interact with sodium channels in physiological processes, affecting various functions in organisms. Exposure to these toxins can lead to symptoms ranging from tingling sensations to respiratory failure and cardiovascular shock, with STX being one of the most potent. The structural diversity of STX derivatives, categorized into carbamate, N-sulfocarbamoyl, decarbamoyl, and deoxydecarbamoyl toxins, offers potential for drug development. The research described in this work aimed to computationally characterize 18 STX derivatives, exploring their reactivity properties within marine sponges using conceptual density functional theory (CDFT) techniques. Additionally, their pharmacokinetic properties, bioavailability, and drug-likeness scores were assessed. The outcomes of this research were the chemical reactivity parameters calculated via CDFT as well as the estimated pharmacokinetic and ADME properties derived using computational tools. While they may not align directly, the integration of these distinct datasets enriches our comprehensive understanding of the compound's properties and potential applications. Thus, this study holds promise for uncovering new pharmaceutical candidates from the considered marine toxins.

Theoretical Analysis of a Three-Component Reaction between Two Diazo Compounds and a Hydroxylamine Derivative: Mechanism, Enantioselectivity, and Effect of Cooperative Catalysis

The mechanism, enantioselectivity, and effect of chiral phosphoric acid (CPA) cocatalyst were investigated by the density functional theory (DFT) for the three-component asymmetric aminohydroxylation between two diazo compounds and a hydroxylamine derivative. This type of cascade process is cooperatively catalyzed by Rh2(OAc)4 and CPA. The obtained results clearly indicate that the first step of the global reaction involves a nucleophilic attack at the nitrogen center of N-hydroxyaniline by rhodium-carbene intermediates producing imines. Subsequently, an enolate intermediate was recognized as the key species generated from the second diazo compound and the leaving benzyl alcohol (BnOH) fragment of the first step and in the presence of the same dirhodium catalyst. Then, the reaction is terminated by the asymmetric Mannich-type addition, delivering the aminohydroxylation products of an S-R conformation with the assistance of chiral phosphoric acid. The distortion/interaction analysis shows that the relative distortions of CPA and the enol play a vital role in the energy ordering of the stereocontrolling transition states (TSs). Furthermore, the influence of different substituents in CPA was fully rationalized by distortion/interaction analysis. This study opens up novel synthetic possibilities and improves the reaction predictability when exploring the related types of cooperatively catalyzed organic transformations.

Exploring marine toxins: comparative analysis of chemical reactivity properties and potential for drug discovery

Marine toxins, produced by various marine microorganisms, pose significant risks to both marine ecosystems and human health. Understanding their diverse structures and properties is crucial for effective mitigation and exploration of their potential as therapeutic agents. This study presents a comparative analysis of two hydrophilic and two lipophilic marine toxins, examining their reactivity properties and bioavailability scores. By investigating similarities among these structurally diverse toxins, valuable insights into their potential as precursors for novel drug development can be gained. The exploration of lipophilic and hydrophilic properties in drug design is essential due to their distinct implications on drug distribution, elimination, and target interaction. By elucidating shared molecular properties among toxins, this research aims to identify patterns and trends that may guide future drug discovery efforts and contribute to the field of molecular toxinology. The findings from this study have the potential to expand knowledge on toxins, facilitate a deeper understanding of their bioactivities, and unlock new therapeutic possibilities to address unmet biomedical needs. The results showcased similarities among the studied systems, while also highlighting the exceptional attributes of Domoic Acid (DA) in terms of its interaction capabilities and stability.

DFT, ADME studies and evaluation of the binding with HSA and MAO-B inhibitory potential of protoberberine alkaloids from Guatteria friesiana: theoretical insights of promising candidates for the treatment of Parkinson's disease

CONTEXT

Parkinson's disease is a chronic neurodegenerative condition that has no cure, characterized by the progressive degeneration of specific brain cells responsible for producing dopamine, a crucial neurotransmitter for controlling movement and muscle coordination. Parkinson's disease is estimated to affect around 1% of the world's population over the age of 60, but it can be diagnosed at younger ages. One of the treatment strategies for Parkinson's disease involves the use of drugs that aim to increase dopamine levels or simulate the action of dopamine in the brain. A class of commonly prescribed drugs are the so-called monoamine oxidase B (MAO-B) inhibitors due to the fact that this enzyme is responsible for metabolizing dopamine, thus reducing its levels in the brain. Studies have shown that berberine-derived alkaloids have the ability to selectively inhibit MAO-B activity, resulting in increased dopamine availability in the brain. In this context, berberine derivatives 13-hydroxy-discretinine and 7,8-dihydro-8-hydroxypalmatine, isolated from Guatteria friesiana, were evaluated via density functional theory followed by ADME studies, docking and molecular dynamic simulations with MAO-B, aiming to evaluate their anti-Parkinson potential, which have not been reported yet. Docking simulations with HSA were carried out aiming to evaluate the transport of these molecules through the circulatory system.

METHODS

The 3D structures of the berberine-derived alkaloids were modeled via the DFT approach at B3LYP-D3(BJ)/6-311 + + G(2df, 2pd) theory level using Gaussian 09 software. Solvation free energies were determined through Truhlar's solvation model. MEP and ALIE maps were generated with Multiwfn software. Autodock Vina software was used for molecular docking simulations and analysis of the interactions in the binding sites. The 3D structure of MAO-B was obtained from the Protein Data Bank website under PDB code 2V5Z. For the interaction of studied alkaloids with human serum albumin (HSA) drug sites, 3D structures with PDB codes 2BXD, 2BXG, and 4L9K were used. Molecular dynamics simulations were carried out using GROMACS 2019.4 software, with the GROMOS 53A6 force field at 100 ns simulation time. The estimation of the ligand's binding free energies was obtained via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method.

Theoretical study of Ponceau S oxidation using the electro-Fenton process under optimal operational conditions

Electrochemical methods as one of the Advanced Oxidation Processes (AOPs) have been applied effectively to the degradation of recalcitrant organic molecules in aqueous solutions. In the present study, the performance of the electro-Fenton (EF) process on the oxidation of Ponceau S(PS) dye was studied. The experimental study performed at the optimal factors like the solution pH, the PS concentration and the ferrous ions dose provided 74.35% of PS degradation. The results, however, showed a decreased removal efficiency of PS when using sodium sulphate as the supporting electrolyte. From a theoretical point of view, the hydroxyl radical being an electron acceptor and the PS dye an electron donor, from a theoretical point of view, the hydroxyl radical being an electron acceptor and the PS dye an electron donor, furthermore, the nitrogen atom 2N being the most nucleophilic site of the PS dye with the most electrophilic site of the hydroxyl radical being the oxygen atom, the first stage of the reaction between PS and the hydroxyl radical was suggested.

Network-Derived Radioresistant Breast Cancer Target with Candidate Inhibitors from Brown Algae: A Sequential Assessment from Target Selection to Quantum Chemical Calculation

Despite significant progress in early detection and treatment, a few aggressive breast cancers still exhibit resistance to therapy. This study aimed to identify a therapeutic target for radioresistant breast cancer (RRbc) through a protein network from breast cancer genes and to evaluate potent phytochemicals against the identified target. Our approach includes the integration of differential expression genes from expression datasets to create a protein network and to use survival analysis to identify the crucial RRbc protein in order to discover a therapeutic target. Next, the phytochemicals sourced from brown algae were screened through molecular docking, ADME (absorption, distribution, metabolism, and excretion), molecular dynamics (MD) simulation, MM-GBSA, and quantum mechanics against the identified target. As a result of our protein network investigation, the proto-oncogene c-KIT (KIT) protein was identified as a potent radioresistant breast cancer target. Further, phytochemical screening establishes that nahocol-A1 from brown algae has high binding characteristics (-8.56 kcal/mol) against the KIT protein. Then, quantum chemical analysis of nahocol-A1 provided insights into its electronic properties favorable for protein binding. Also, MD simulation comprehends the conformational stability of the KIT-nahocol-A1 complex. Overall, our findings suggest nahocol-A1 could serve as a promising therapeutic candidate for radioresistant breast cancer.

Sulfur Centered Hydrogen Bonding in Thioglycolic Acid and Its Clusters: A Computational Exploration

The conformational landscape of thioglycolic acid (TGA) was investigated by using the CCSD/cc-pVTZ level of theory. The GGC conformer was identified as the global minimum, followed by the GAC conformer. The calculated rotational constant for the GGC conformer exhibited good agreement with the previously reported experimental results. Subsequently, the study delved into the exploration of sulfur-centered hydrogen bonding in TGA's dimer and trimer clusters, employing the CCSD/cc-pVDZ level of theory. These clusters revealed the participation of both oxygen and sulfur atoms in noncovalent H-bonding, contributing to their stability. The presence of these noncovalent interactions in TGA clusters was elucidated through Atoms in Molecule (AIM), reduced density gradient (RDG), and natural bond order (NBO) analysis, while electrostatic potential (ESP) charge and vibrational mode analysis further supported these findings.

Computational Discovery of Marine Molecules of the Cyclopeptide Family with Therapeutic Potential

Stellatolides are natural compounds that have shown promising biological activities, including antitumor, antimicrobial, and anti-inflammatory properties, making them potential candidates for drug development. Chemical Reactivity Theory (CRT) is a branch of chemistry that explains and predicts the behavior of chemical reactions based on the electronic structure of molecules. Conceptual Density Functional Theory (CDFT) and Computational Peptidology (CP) are computational approaches used to study the behavior of atoms, molecules, and peptides. In this study, we present the results of our investigation of the chemical reactivity and ADMET properties of Stellatolides A-H using a novel computational approach called Conceptual DFT-based Computational Peptidology (CDFT-CP). Our study uses CDFT and CP to predict the reactivity and stability of molecules and to understand the behavior of peptides at the molecular level. We also predict the ADMET properties of the Stellatolides A-H to provide insight into their effectiveness, potential side effects, and optimal dosage and route of administration, as well as their biological targets. This study sheds light on the potential of Stellatolides A-H as promising candidates for drug development and highlights the potential of CDFT-CP for the study of other natural compounds and peptides.

Talarolide A and Talaropeptides A-D: Potential Marine-Derived Therapeutic Peptides with Interesting Chemistry and Biological Activity Studied through Density Functional Theory (DFT) and Conceptual DFT

Molecules sourced from marine environments hold immense promise for the development of novel therapeutic drugs, owing to their distinctive chemical compositions and valuable medicinal attributes. Notably, Talarolide A and Talaropeptides A-D have gained recent attention as potential candidates for pharmaceutical applications. This study aims to explore the chemical reactivity of Talarolide A and Talaropeptides A-D through the application of molecular modeling and computational chemistry techniques, specifically employing Conceptual Density Functional Theory (CDFT). By investigating their chemical behaviors, the study seeks to contribute to the understanding of the potential pharmacological uses of these marine-derived compounds. The molecular geometry optimizations and frequency calculations were conducted using the Density Functional Tight Binding (DFTBA) method. This was followed by a subsequent round of geometry optimization, frequency analysis, and computation of electronic properties and chemical reactivity descriptors. We employed the MN12SX/Def2TZVP/H2O model chemistry, utilizing the Gaussian 16 program and the SMD solvation model. The analysis of the global reactivity descriptors arising from CDFT was achieved as well as the graphical comparison of the dual descriptor DD revealing the areas of the molecules with more propensity to suffer a nucleophilic or electrophilic attack. Additionally, Molinspiration and SwissTargetPrediction were considered for the calculation of molecular characteristics and predicted biological targets. These include enzymes, nuclear receptors, kinase inhibitors, GPCR ligands, and ion channel modulators. The graphical results show that Talarolide A and the Talaropeptides A-D are likely to behave as protease inhibitors.

Halogen Bonding Involving Isomeric Isocyanide/Nitrile Groups

2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···Cisocyanide or I···Nnitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor.

A molecular electron density theory study of asymmetric Diels-Alder [4 + 2] reaction's mechanism of furan with three substituted alkynes (5-R substituted-3-(3-(phenylsulfonyl)-propioloyl)-oxazolidin-2-one)

CONTEXT

The [4 +2 ] cycloaddition reactions between furan and three substituted alkynes (5-R-substituted-3-(3-(phenylsulfonyl)-propioloyl)-oxazolidin-2-one) have been investigated using the MEDT approach. Reactivity indices, reaction pathways, and activation energies are calculated. In an investigation of conceptual DFT indices, furan acts as a nucleophile, while the three substituted alkynes (5-R-substituted-3-(3-(phenylsulfonyl)-propioloyl)-oxazolidin-2-one) function as electrophiles in this reaction. The cycloaddition is regioiselective, as demonstrated by the activation and reaction energies, in clear agreement with the experiment's results. Hetero Diels-Alder [4 + 2] cycloadditions occur following a non-concerted two stages one-step molecular mechanism.

METHODS

For the purpose of this study, all calculations were performed using the Gaussian 09 software. Optimization was achieved through Berny's computational gradient optimization method, employing the B3LYP functional and the 6-31G(d) basis set. Analysis of both local and global reactivity indices provided insights into the reactivity tendencies of the reactants, distinguishing between electrophilic and nucleophilic characteristics via Parr functions. Frequency calculations were employed to identify and characterize stationary points, with transition states indicated by a single imaginary frequency and positive values of all frequencies for reactants and product. The electron localization function (ELF) was investigated using the Multiwfn software within the context of topological analyses.

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

[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.

Halogen Bond to Experimentally Significant N-Heterocyclic Carbenes (I, IMe2, IiPr2, ItBu2, IPh2, IMes2, IDipp2, IAd2; I = Imidazol-2-ylidene)

The subjects of the article are halogen bonds between either XCN or XCCH (X = Cl, Br, I) and the carbene carbon atom in imidazol-2-ylidene (I) or its derivatives (IR2) with experimentally significant and systematically increased R substituents at both nitrogen atoms: methyl = Me, iso-propyl = iPr, tert-butyl = tBu, phenyl = Ph, mesityl = Mes, 2,6-diisopropylphenyl = Dipp, 1-adamantyl = Ad. It is shown that the halogen bond strength increases in the order Cl < Br < I and the XCN molecule forms stronger complexes than XCCH. Of all the carbenes considered, IMes2 forms the strongest and also the shortest halogen bonds with an apogee for complex IMes2⋯ICN for which D0 = 18.71 kcal/mol and dC⋯I = 2.541 Å. In many cases, IDipp2 forms as strong halogen bonds as IMes2. Quite the opposite, although characterized by the greatest nucleophilicity, ItBu2 forms the weakest complexes (and the longest halogen bonds) if X ≠ Cl. While this finding can easily be attributed to the steric hindrance exerted by the highly branched tert-butyl groups, it appears that the presence of the four C-H⋯X hydrogen bonds may also be of importance here. Similar situation occurs in the case of complexes with IAd2.

Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3,3,3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2-(dimethylamino)-1H-indene-1,3(2H)-dione (AY11) and trans(E)-3,3,3-trifluoro-1-nitroprop-1-ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6-31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non-concerted two-stage one-step mechanism. Finally, non-covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta-endo cycloadduct.