SERS-Based Sensor Using Subnanometric Copper-Silver Mixed Clusters Ag(8-n)Cun (n = 0-8) for Pyridine: A DFT Study.

Surface-enhanced Raman spectroscopy (SERS) is a powerful Raman technique that provides high selectivity and sensitivity in analyzing the intermolecular interaction of a target compound adsorbed on the surface of a noble nanomaterial, i.e., silver, gold, or copper. Although copper presents a better SERS enhancement than gold and silver, its oxidation in the air is much easier than that of gold and silver. A mixed material between these metals may potentially improve the SERS signal enhancement in this context. In this work, we evaluated the SERS spectra of pyridine (Py) adsorbed on the copper-silver mixed clusters Ag(8-n)Cun (n = 0-8) using density functional theory (DFT) at the PBE functional. The cc-pVDZ-PP basis set was chosen for Ag and Cu, while the cc-pVDZ basis set was used for C, N, and H atoms. Geometrical and electronic structures of the mixed clusters and the Py adsorption configuration on these clusters were computed. The calculated SERS spectra then revealed the influence of the Ag/Cu mixing ratio on the SERS enhancement. As a result, the substituted copper atoms on the silver cluster turned out to be favorable adsorption sites for Py. Interestingly, when the number of Cu atoms increased from n = 0 (pure Ag8 cluster) to n = 5 (Ag3Cu5 cluster), the ring stretching peak (1590 cm-1) of Py significantly increased from 20 to 120 au and then saturated around this value despite increasing the Cu atom number to 8 (pure Cu8 cluster). This observation was extended for other ligands such as pyrazine and 3H-pyrrole. TD-DFT was then employed to clarify the chemical enhancement mechanism. The results obtained hopefully provide helpful information for the design of analytical sensors with lower costs.

Theoretical insights into the HO●-induced oxidation of chlorpyrifos pesticide: Mechanism, kinetics, ecotoxicity, and cholinesterase inhibition of degradants.

The oxidation of the common pesticide chlorpyrifos (CPF) initiated by HO● radical and the risks of its degradation products were studied in the gaseous and aqueous phases via computational approaches. Oxidation mechanisms were investigated, including H-, Cl-, CH3- abstraction, HO●-addition, and single electron transfer. In both phases, HO●-addition at the C of the pyridyl ring is the most energetically favorable and spontaneous reaction, followed by H-abstraction reactions at methylene groups (i.e., at H19/H21 in the gas phase and H22/H28 in water). In contrast, other abstractions and electron transfer reactions are unfavorable. However, regarding the kinetics, the significant contribution to the oxidation of CPF is made from H-abstraction channels, mostly at the hydrogens of the methylene groups. CPF can be decomposed in a short time (5-8 h) in the gas phase, and it is more persistent in natural water with a lifetime between 24 days and 66 years, depending on the temperature and HO● concentration. Subsequent oxidation of the essential radical products with other oxidizing reagents, i.e., HO●, NO2●, NO●, and 3O2, gave primary neutral products P1-P15. Acute and chronic toxicity calculations estimate very toxic levels for CPF and two degradation products, P7w and P12w, in aquatic systems. The neurotoxicity of these products was investigated by docking and molecular dynamics. P7w and P12w show the most significant binding scores with acetylcholinesterases, while P8w and P13w are with butyrylcholinesterase enzyme. Finally, molecular dynamics illustrate stable interactions between CPF degradants and cholinesterase enzyme over a 100 ns time frame and determine P7w as the riskiest degradant to the neural developmental system.

New insight into environmental oxidation of phosmet insecticide initiated by HO˙ radicals in gas and water - a theoretical study.

Phosmet is an organophosphorus insecticide widely used in agriculture to control a range of insects; recently, it was banned by the European Union in 2022 due to its harmful effects. However, its environmental degradation and fate have not yet been evident. Thus, phosmet oxidation by HO˙ radicals was theoretically studied in this work using the DFT approach at the M06-2X/6-311++G(3df,3pd)//M06-2X/6-31+G(d,p) level of theory. Three different mechanisms were considered, including formal hydrogen transfer (FHT), radical adduct formation (RAF), and single electron transfer (SET). The mechanisms, kinetics, and lifetime were studied in the gas and aqueous phases, in addition to its ecotoxicity evaluation. The results show that FHT reactions were dominant in the gas phase, while RAF was more favourable in the aqueous phase at 298 K, while SET was negligible. The branching ratio indicated that H-abstractions at the methyl and the methylene groups were the most predominant, while the most favourable HO˙-addition was observed at the phosphorus atom of the dithiophosphate group. The overall rate constant values varied from 1.2 × 109 (at 283 K) to 1.40 × 109 M-1 s-1 (at 323 K) in the aqueous phase and from 6.29 × 1010 (at 253 K) to 1.32 × 1010 M-1 s-1 (at 323 K) in the gas phase. The atmospheric lifetime of phosmet is about 6 hours at 287 K, while it can persist from a few seconds to several years depending on the temperature and [HO˙] concentration in the aqueous environment. The QSAR-based ecotoxicity evaluation indicates that phosmet and its degradation products are all dangerous to aquatic organisms, although the products are less toxic than phosmet. However, they are generally developmental toxicants and mutagenicity-negative compounds.

On The Radical Scavenging and DNA Repairing Activities by Natural Oxygenated Diterpenoids: Theoretical Insights.

Diterpenoids are abundant and important compounds in Euphorbia species owing to their structural diversity; therefore, in this study, we investigate the modern-concept antioxidant activities, including free-radical scavenging and oxidative DNA damage repairing, of highly oxygenated diterpenoids originating from the aerial part of Euphorbia helioscopia. Four compounds with structural types of ent-abietane, containing a fused furan ring in their structures, including euphelionolide A (1), euphelionolide D (2), euphelionolide I (3), and euphelionolide L (4) are selected. First, the radical-scavenging activity of these compounds was evaluated with two typical radicals HOO• and HO• in water and pentyl ethanoate (PEA, to mimic lipid environment) via three main mechanisms, namely, hydrogen atom transfer (HAT), radical adduct formation (RAF), and single electron transfer. It is found that the studied compounds are able to scavenge free radicals at multiple reactive sites favorably via HAT and RAF mechanisms, in which the former dominates in the case with HOO• while both mechanisms are competitive in the reaction with HO•. Second, chemical repairing of DNA damage is modeled with the H-atom and single electron being transferred from the studied molecules to damaged 2'-deoxyguanosine (2dG) (i.e., 2dG• radicals and 2dG•+ radical cation). Among the four compounds, euphelionolide A is shown as the most effective radical scavenger and also the highest potential species for chemical repairing of radical-damaged DNA in both water and PEA.

New insights into the competition between antioxidant activities and pro-oxidant risks of rosmarinic acid.

Direct and indirect antioxidant activities of rosmarinic acid (RA) based on HOO˙/CH3OO˙ radical scavenging and Fe(iii)/Fe(ii) ion chelation were theoretically studied using density functional theory at the M05-2X/6-311++G(2df,2p) level of theory. First, four antioxidant mechanisms including hydrogen atom transfer (HAT), radical adduct formation (RAF), proton loss (PL) and single electron transfer (SET) were investigated in water and pentyl ethanoate (PEA) phases. Regarding the free radical scavenging mechanism, HAT plays a decisive role with overall rate coefficients of 1.84 × 103 M-1 s-1 (HOO˙) and 4.49 × 103 M-1 s-1 (CH3OO˙) in water. In contrast to PL, RAF and especially SET processes, the HAT reaction in PEA is slightly more favorable than that in water. Second, the [Fe(iii)(H2O)6]3+ and [Fe(ii)(H2O)6]2+ ion chelating processes in an aqueous phase are both favorable and spontaneous especially at the O5, site-1, and site-2 positions with large negative Δr G 0 values and great formation constant K f. Finally, the pro-oxidant risk of RA- was also considered via the Fe(iii)-to-Fe(ii) complex reduction process, which may initiate Fenton-like reactions forming reactive HO˙ radicals. As a result, RA- does not enhance the reduction process when ascorbate anions are present as reducing agents, whereas the pro-oxidant risk becomes remarkable when superoxide anions are found. The results encourage further attempts to verify the speculation using more powerful research implementations of the antioxidant activities of rosmarinic acid in relationship with its possible pro-oxidant risks.

SERS Chemical Enhancement of 2,4,5-Trichlorophenoxyacetic Acid Adsorbed on Silver Substrate.

Surface-enhanced Raman spectroscopy (SERS) was employed to gain an understanding of the chemical enhancement mechanism of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), an Agent Orange, adsorbed on a silver substrate surface. Experimental measurements were performed using a micro-Raman spectrophotometer with an excitation wavelength of 532 nm and successfully detected 2,4,5-T at a relatively low concentration of 0.4 nM. Density functional theory (DFT) calculations on the interactions of the 2,4,5-T molecule with some small silver clusters, Agn with n = 4, 8, and 20, as well as with extended Ag surfaces, demonstrate that the most stable adsorption configuration is formed via coordination of Cl9 sites and carbonyl C═O group on the 2,4,5-T ligand to the Ag atoms on surfaces. Analyses of charge transfer mechanism and frontier orbitals distributions show an electron transfer from 2,4,5-T to the cluster in the ground state, and an inversed trend occurs for the excited singlet state process, consequently leading to a chemical enhancement of SERS signals. The obtained results are of importance for subsequent work in guiding the design of mobile sensors specifically used for services of rapid screening and detection of these toxic compounds present in the environment, as well as agricultural and food products. Extensive computations pointed out that small silver clusters, in particular of Ag20 size, can be used as appropriate models for a metal nanoparticle surface.

Antioxidant and UV-radiation absorption activity of aaptamine derivatives - potential application for natural organic sunscreens.

Antioxidant and UV absorption activities of three aaptamine derivatives including piperidine[3,2-b]demethyl(oxy)aaptamine (C1), 9-amino-2-ethoxy-8-methoxy-3H-benzo[de][1,6]naphthyridine-3-one (C2), and 2-(sec-butyl)-7,8-dimethoxybenzo[de]imidazo[4,5,1-ij][1,6]-naphthyridin-10(9H)-one (C3) were theoretically studied by density functional theory (DFT). Direct antioxidant activities of C1-C3 were firstly evaluated via their intrinsic thermochemical properties and the radical scavenging activity of the potential antioxidants with the HOO˙/HO˙ radicals via four mechanisms, including: hydrogen atom transfer (HAT), single electron transfer (SET), proton loss (PL) and radical adduct formation (RAF). Kinetic calculation reveals that HOO˙ scavenging in water occurs via HAT mechanism with C1 (k app, 7.13 × 106 M-1 s-1) while RAF is more dominant with C2 (k app, 1.40 × 105 M-1 s-1) and C3 (k app, 2.90 × 105 M-1 s-1). Antioxidant activity of aaptamine derivatives can be classified as C1 > C3 > C2. Indirect antioxidant properties based on Cu(i) and Cu(ii) ions chelating activity were also investigated in aqueous phase. All three studied compounds show spontaneous and favorable Cu(i) ion chelating activity with ΔG 0 being -15.4, -13.7, and -15.7 kcal mol-1, whereas ΔG 0 for Cu(ii) chelation are -10.4, -10.8, and -2.2 kcal mol-1 for C1, C2 and C3, respectively. In addition, all compounds show UVA and UVB absorption; in which the excitations are determined mostly as π-π* transition. Overall, the results suggest the potential applications of the aaptamines in pharmaceutics and cosmetics, i.e. as a sunscreen and antioxidant ingredient.

Antioxidant and Anticancer Properties of Functionalized Ferrocene with Hydroxycinnamate Derivatives-An Integrated Experimental and Theoretical Study.

Two ferrocenyl derivatives, Fc-CA and Fc-FA, were synthesized by a condensation reaction between the amino ferrocene and hydroxycinnamic acids, that is, caffeic acid (CA) and ferulic acid (FA). The structures and purity of all compounds were characterized by 1H- and 13C NMR spectroscopies, Mass spectrometry (MS), and elemental analysis. The antioxidant properties of Fc-CA and Fc-FA and of its ligand were studied for free radical scavenging activity toward DPPH•, superoxide anion (O2•-), NO•, and ABTS•+ by UV-vis and electron spin resonance spectroscopies. The cytotoxicity of Fc-CA and Fc-FA against MCF-7 and MDA-MB-231 breast cancer cells and MRC-5 human lung fibroblasts cell was higher than that of cisplatin. The geometry and electronic structures of all compounds were then simulated using density functional theory at M05-2X/6-311+G(d,p) level of theory. Thermodynamics of the free radical quenching reactions by common mechanisms reveal the higher antioxidant properties of the Fc-CA and Fc-FA in comparison to their ligands. An in-depth study of the free radical scavenging activity against HOO• and HO• radicals was performed for two of the most favorable and competitive mechanisms, the hydrogen transfer (either hydrogen atom transfer or proton-coupled electron transfer mechanisms) and the radical adduct formation. The in silico studies indicated that ferrocenyl derivatives exhibited prominent binding affinity to protein models in comparison to CA and FA. Their dock scores were notable at ligand binding sites of ERα, Erß, and JAK2 proteins. Dock pose analysis also shed light into the possible mechanism of action for the studied compounds.

Insight into Antioxidant and Photoprotective Properties of Natural Compounds from Marine Fungus.

This computational and experimental work aims to elucidate physicochemical and photophysical natures of free radical scavenging and ultraviolet radiation (UVR) filtering activities of five terpenoids available in the extract of marine fungus. The antioxidant activities of ochraceopone F (C1), aspertetranone D (C2), cycloechinulin (C3), wasabidienone E (C4), and mactanamide (C5) are evaluated by using density functional theory (DFT) at the M05-2X/6-311++G(d,p) level of theory in the gas phase, water, and pentyl ethanoate (PEA). Double antioxidant mechanisms allowing the second (H+/e-) donation such as double hydrogen atom transfer (dHAT), double single electron transfer-proton transfer (dSET-PT), and double sequential proton loss-electron transfer (dSPL-ET) are considered. Reaction enthalpies (ΔrH0), standard Gibbs free energies (ΔrG0) and potential energy surfaces of reactions toward HOO• radical are then established to evaluate the hydrogen transfer (HT) and radical adduct formation (RAF) mechanisms. The computational results are supported by DPPH• and ABTS•+ antioxidant essays. Results show that all compounds C1-C5 are able to scavenge two free radicals via dHAT, dSET-PT, and dSPL-ET mechanisms. Among the compounds, C3 and C4 represent the most potential antioxidants, especially via HAT and RAF mechanisms in all the reaction media. Their rate constants for both HAT and RAF reactions are remarkably higher than that of Trolox and ascorbic acid. The kinetic calculations on activation Gibbs free energies (ΔG⧧) and rate constants (kTST) based on conventional transition state theory (TST) reveal that HAT and RAF processes are in competition in solvents. Photophysical processes occurring during UVR exposure are investigated using the time dependent density functional theory (TD-DFT) combined with UV-vis experiments. The obtained results highlight the promising activities of C1-C5 in UVR absorption in the ranges of UVA and UVB. Among them, C3 and C4 also show better UV absorption properties with the easiest excitations (band gaps equal to 4.06 and 3.65 eV). This study suggests the natural candidates possibly used in organic sunscreen.

Experimental and theoretical investigation of cyclometalated phenylpyridine iridium(iii) complex based on flavonol and ibuprofen ligands as potent antioxidant.

An Ir(iii) complex was synthesized using mixed ligands of biological importance, namely ibuprofen, flavonol and 2-phenylpyridine. The compound was characterized by 1H-NMR, 13C-NMR and TOF-MS spectroscopies and elemental analysis. Structures of the complex and its ligands were also calculated by density functional theory using B3LYP/Lanl2dz//6-31G(d) level of theory. Analyses of electrostatic potential, natural population, and frontier orbitals of the molecules as well as the calculation of intrinsic thermochemical properties such as bond dissociation enthalpy, ionization potential, electron affinity and proton affinity in the gas phase and in solvents (water and pentylethanoate) give the first indication that the complex is a potential antioxidant. The latter even shows better antioxidant capacity than the parent ligands. The antioxidant properties of the complex and its ligands were experimentally evaluated by studying the free radical scavenging activity towards HO˙, NO˙, DPPH˙ and ABTS˙+ radicals. Further computational work on the antioxidant processes such as the single electron transfer, the proton loss, the formal hydrogen transfer (FHT) and the radical adduct formation reactions was conducted. Results show that the FHT reaction is the mechanism responsible for the radical scavenging activity of the complex towards HO˙, HOO˙, NO˙ and DPPH˙ radicals while ABTS˙+ seems to be scavenged by an electron-donating mechanism. The FHT was further determined as a hydrogen-atom transfer but not a proton-couple electron transfer mechanism.

Reinvestigation of the M(II) (M = Ni, Co)/tetrathiafulvalenetetracarboxylate system using high-throughput methods: isolation of a molecular complex and its single-crystal-to-single-crystal transformation to a two-dimensional coordination polymer.

A high-throughput methodology combined with X-ray powder diffraction measurements was used to investigate the reactivity of the TetraThiaFulvalene TetraCarboxylic acid ((TTF-TC)H(4)) with divalent metals (M = Ni, Co) under various reaction conditions (stoichiometry, pH, temperature). Two new crystalline phases were identified and then studied by single crystal X-ray diffraction. Whereas the first one appears to be a simple salt, the second one, formulated {[M(H(2)O)(4)](2)(TTF-TC)}·4H(2)O, is built of 2:1 M:TTF-TC molecular complexes and labeled MIL-136(Ni, Co) (MIL stands for Materials Institute Lavoisier). The combination of thermogravimetric analysis and thermodiffraction studies reveals that MIL-136(Ni) exhibits a complex dehydration behavior. Indeed, a partial dehydration/rehydration process led to the single-crystal-to-single-crystal transformation of the molecular compound in a two-dimensional coordination polymer formulated {[Ni(2)(H(2)O)(5)(TTF-TC)]}·H(2)O (MIL-136'(Ni)). Magnetic and redox properties of MIL-136(Ni, Co) were investigated. Magnetic measurements indicate that all the magnetic coupling, intra- and intermolecular, are very weak; thus, the magnetic data of MIL-136(Ni, Co) have been interpreted in term of single-ion spin orbit coupling. Solid state cyclic voltammetry of MIL-136(Ni, Co) presents three reversible waves which were assigned to the redox activity of the TTF core and the metallic cations. In contrast to solids based on TTF linkers and alkaline ions, the MIL-136(Ni, Co) complexes do not act as excellent positive electrode materials for Li batteries, but present two reversible electron oxidation of the TTF core. These observations were tentatively related to the strength of the metal-carboxylate bond.

3-D coordination polymers based on the tetrathiafulvalenetetracarboxylate (TTF-TC) derivative: synthesis, characterization, and oxidation issues.

The reactivity of the redox-active tetracarboxylic acid derived from the tetrathiafulvalene (TTF-TC)H(4) with alkaline cations (K, Rb, Cs) is reported. The exploration of various experimental parameters (temperature, pH) led to the formation of four crystalline three-dimensional coordination polymers formulated M(2)(TTF-TC)H(2) (M = K, Rb, Cs), denoted MIL-132(K), MIL-133(isostructural K, Rb), and MIL-134(Cs). Thermogravimetric analysis and thermodiffraction show that all of the solids are thermally stable up to 150-200 degrees C in the air. In order to exploit the possibility of oxidation of the organic linker in TTF-based compounds, they were employed as positive electrodes in a classical lithium cell. A highly reversible cyclability was achieved at high current density (10 C) with a reasonable performance (approximately 50 mAh g(-1)). Finally, combined electro-(sub)hydrothermal synthesis was used to prepare a fifth 3-D coordination polymer formulated K(TTF-TC)H(2) (denoted MIL-135(K)), this time not based on the neutral TTF-TC linker but its radical, oxidized form TTF-TC(+*). This solid is less thermally stable than its neutral counterparts but exhibits a semiconducting behavior, with a conductivity at room temperature of about 1 mS cm(-1).