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.

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.

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.

Radical Scavenging Activity of Natural-Based Cassaine Diterpenoid Amides and Amines.

The radical scavenging capacities of four new cassaine diterpenoid amides including 3ß-hydroxydinorerythrosuamide (1), 3ß-acetoxydinorerythrosuamide (2), 3ß-tigloyloxydinorerythrosuamide (3), and 6α-hydroxydinorcassamide (4) present in leaf extract and four new cassaine diterpenoid amines namely erythroformine A (5), erythroformine B (6), 6α-hydroxy-nor-cassamine (7), and nor-erythrosuamine (8) recently identified in the extract of the bark of Erythrophleum fordii were elucidated using density functional theory (DFT) method. Different thermochemical properties characterizing antioxidant potential including bond dissociation enthalpy (BDE), proton affinity (PA), and adiabatic ionization potential (IP) were calculated at the B3LYP/6-311G(d,p) level of theory. Scavenging reaction mechanisms of cassaine diterpenes toward HOO• radical including formal hydrogen transfer (FHT; either hydrogen atom transfer (HAT) or proton coupled electron transfer (PCET)), radical adduct formation (RAF), single electron transfer (SET), and proton transfer (PT) were studied in the gas phase, water, and benzene. The potential energy profiles and kinetic calculations for the FHT and RAF reactions were calculated at 298.15 K. The results showed that all the studied compounds present strong antioxidant activity via HAT mechanism with BDEs varying from 69.4 to 77.9 kcal/mol. While solvents have only a slight effect on HAT and RAF mechanisms, SET and PT reactions are likely to occur in polar media. Among the studied compounds, 3 is the most reactive one both for HAT (H-abstraction at C7, Δ H -11.3 kcal/mol) and for RAF (radical addition at C13 = C15 bond, Δ H -5.2 kcal/mol) reactions. The rate constants of these reactions are also comparable with several referenced antioxidants such as Trolox and ascorbic acid.

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.

Hydroxyl radical-initiated decomposition of metazachlor herbicide in the gaseous and aqueous phases: Mechanism, kinetics, and toxicity evaluation.

The oxidation of widely-used herbicide metazachlor (MTZ) by hydroxyl radical (HO•) in the gas and the aqueous phases was investigated in terms of mechanistic and kinetic behaviors using the M06-2X/6-311++G (3df, 3pd)//M06-2X/6-31 + G (d,p) level of theory over the temperature range 250-400 K. The formal hydrogen transfer, HO•-addition, and single electron transfer mechanisms were considered. The overall rate constants in the gas phase range from 8.40 × 1010 to 8.31 × 109 M-1 s-1 at the temperature from 250 to 400 K, respectively, while the ones in the aqueous phase are close to diffusion-controlled rates, with diffusion-corrected rate constants being 1.31 × 109 to 1.27 × 109 M-1 s-1. The formal hydrogen transfer mechanism is the most dominant in the gas phase, whereas the HO•-addition is the most favorable in the aqueous phase. The H-abstraction at two methyl groups and the HO•-addition to C11 and C12 atoms (pyrazole ring), C16 and C18 atoms (benzyl ring) are significant. The short lifetime in the environment, equal to only 4.16 h, requires more attention to this herbicide compound, whereas its lifetime in the aqueous condition varies sharply from half second to several thousand days depending on the HO• concentration. The ecotoxicity estimation of MTZ and its principal transformation products to aquatic organisms suggests that they are harmful or toxic substances. Moreover, the MTZ is a developmental toxicant and mutagenicity-positive, while its decomposed products are developmental toxicants with no mutagenic toxicity. Their bioaccumulation in aquatic organisms is negligible.

On the free radical scavenging and metallic ion chelating activities of pyridoxal - Could the pro-oxidant risk be competitive?

Primary and secondary antioxidant activities of pyridoxal have been investigated by using density functional theory (DFT) at the M05-2X level combined with 6-311++G(d,p) basis set for non-metallic atoms and LanL2DZ for metallic ions. The former has been examined by its free radical scavenging activity towards HOO●, HO●, and NO2●via different mechanisms including formal hydrogen transfer (FHT), proton transfer (PT), single electron transfer (SET), and radical adduct formation (RAF). The latter has been accomplished through its transition metal-chelating ability with Fe(III)/Fe(II) and Cu(II)/Cu(I) ions. The results show that pyridoxal illustrates as an efficient radical scavenger, especially, for HO● and NO2● in water. The overall rate constants (koverall) for the reactions with HOO●, HO●, and NO2● radicals are 1.30 × 104, 5.76 × 109, and 1.43 × 109 M-1s-1, respectively. The SET from the anionic state is the most dominant for the HOO● and NO2● scavenging reactions, while both RAF and SET contribute largely to the reaction with highly reactive HO● radicals. Moreover, the anionic form of pyridoxal demonstrates a better role as a metal chelator than the neutral. However, the pro-oxidant risks of the formed complexes could be observed if there are superoxide radical anion (O2●-) and ascorbate (Asc-) in aqueous media.

Oxidation of l-leucine amino acid initiated by hydroxyl radical: are transition metal ions an enhancement factor?

Hydroxyl radical (HO·) formation initiated by the Fenton-type reactions of Fe and Cu complexes of l-leucine (Leu) amino acid as well as its oxidation reaction by HO· was computationally investigated by using the density functional theory method at the M05-2X/6-311++G(3df,2pd)//M05-2X/6-311++G(d,p) level of theory in the aqueous phase. The results showed that dipole-salt is the main form of Leu in the physiological condition. Leu exhibits high chelating potential towards both Fe(III)/Fe(II) and Cu(II)/Cu(I) ions with the most favourable coordinating positions at two oxygen atoms of the -COO functional group. Furthermore, the Leu-ions complexes show a high risk of HO· formation via Fenton-like reactions, especially when ascorbate anion exists in the environment as a reducing agent. Finally, the oxidation reaction of l-leucine by HO· demonstrated a relatively high overall apparent reaction rate, k overall, being 1.18 × 109 M-1 s-1, in which formal hydrogen transfer reactions of the dipole-salt form occur as the primary mechanism. Consequently, the Leu oxidation by HO· radical can be promoted by the Fenton reaction enhancement of its transition metal complexes.

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.

Is Vitamin A an Antioxidant or a Pro-oxidant?

Antioxidant efficiency of all-trans-retinol has been studied on the basis of characteristic thermochemical properties using density functional theory. The influence of the solvent polarity has also been evaluated. It is found that retinol may act in parallel as an effective antioxidant via H atom donating as well as a pro-oxidant in yielding reactive hydroxyl radical. In fact, the lowest values of bond dissociation enthalpy were found at the C18-H and C18-OH positions. Retinol was also determined to be a good electron donor but bad acceptor in the single electron transfer (ET) reaction with hydroperoxyl (HOO•) radical. In addition, potential energy surfaces of H atom transfer (HAT) and radical adduct formation (RAF) reactions between retinol and HOO• radical were also investigated in the gas phase and in the solvent. The results demonstrated that the RAF mechanism was generally more predominant than ET and HAT ones. The most favored radical addition position was found at the C2═C3 double bond in the cyclohexenyl ring. Moreover, the radical scavenging reactivity via RAF reactions was strongly exergonic and thermodynamically feasible while the ET one was endergonic. Natural bond orbital analysis showed that the lone pairs of electrons on the oxygen atom of the HOO• radical were donated to the unoccupied antibonding orbital of transferred H atom in HAT reactions. In contrast, in the case of RAF reactions, strong interactions between 2p orbitals on oxygen atoms of the radical and the π orbital of the double bond on the retinol molecule were recognized. The results obtained in this work were in agreement with previous experimental observations.

Functionalization of fullerene via the Bingel reaction with α-chlorocarbanions: an ONIOM approach.

Two-layer ONIOM method at the ONIOM(B3LYP/6-31G(d):PM6) level of theory was applied to study the cycloaddition reaction of α-chlorocarbanions (CR2Cl(─), where R is H, Cl, CH3 CN, and NO2) and fullerene. The results show that the reaction pathways depend on the electron withdrawing functional groups or the electron donating functional groups contained in the α-chlorocarbanions. The energy profile analysis reveals that functionalization of fullerene by CCl3 (─), C(CH3)2Cl(─), and CH2Cl(─) is more favorable than by C(CN)2Cl(─) and C(NO2)2Cl(─) in terms of the thermodynamic point of view.