DFT study on the selective complexation of meso-2,3-dimercaptosuccinic acid with toxic metal ions (Cd2+, Hg2+ and Pb2+) for pharmaceutical and biological applications

Binding mechanism of metal ions (Ca2+, Cu2+ and Mg2+) with tetrapeptide FFDR: A combined experimental and quantum chemistry approach

A previous study demonstrated that a tetrapeptide FFDR derived from coix seed possesses antioxidant properties. In continuation of the study, Density Functional Theory (DFT) was employed to investigate the molecular-level complexation behaviour of FFDR with Ca2+, Cu2+, and Mg2+. DFT predictions were validated using spectroscopy and cellular model. The electronic properties revealed that Mg-FFDR, with its lower energy gap (1.733 eV), exhibits higher reactivity compared to Ca-FFDR which displayed higher stability (8.180 eV). The Quantum Theory of Atoms in Molecules (QTAIM) showed positive Laplacian values for all metal‑oxygen bonds, indicating the presence of coordination bonds characteristic of closed-shell interactions. Results from 1H NMR spectra revealed J-coupling patterns consistent with metal coordination for Mg and Ca-peptide complexes. FTIR spectra displayed distinct changes in the vibrational frequencies of functional groups involved in metal binding for all complexes. Both Mg-FFDR and Ca-FFDR demonstrated significant ROS scavenging activities, and enhanced SOD and CAT activities in HepG2 cells. These findings serve as a baseline for the rational design of metal-peptide complexes as functional foods or nutraceuticals.

Pyrazinamide-based Co(II), Ni(II) and Cu(II) complexes: DFT exploration of structure, reactivity properties and in silico ADMET profiles

CONTEXT

In this paper, we present a theoretical study on the complexation of Co(II), Ni(II), and Cu(II) with a pyrazinamide ligand (PZA), which plays an important role in the treatment of tuberculosis and has biological and pharmacological benefits. It is a hybrid organic/inorganic material involving coordination between a metal ion and PZA ligand containing different coordination sites. This allows it to have different binding modes with metal ions and, therefore, provides a versatile ability to coordinate with metals. This study aimed to optimize the structures of the [M(PZA)2Cl2] complexes using density functional theory (DFT) at the B3LYP/6-311G + (d,p) level and the M06-2X functional is a high-nonlocality functional of double the amount of nonlocal exchange 2X. Various properties, including geometrical parameters, natural bonding orbital (NBO) to determine atomic charges, HOMO-LUMO energies, electronic properties, reactivity (ELF, LOL), NCI-RDG, and molecular electrostatic potential (MEP) on the surfaces of key metal-PZA complexes were determined and described. The AIM method has also been used to examine the chemical bonds. Furthermore, an in silico analysis aiming to explore the ADMET profiles of the compounds under investigation revealed promising aqueous solubility, oral bioavailability and gastrointestinal absorption, in addition to favorable druglikeness non-toxic and non-carcinogenic characteristics.

METHODS

The DFT method was carried out using Gaussian 09 software and GaussView 5.0. Avogadro software was used to define the geometry of the complexes. The Multiwfn program was used to produce scatter plots of the reduced density gradient (RDG), non-covalent interactions (NCI), ELF, LOL, and to define the parameters selected for the topological analysis of the BCPs using Bader's AIM.

Revealing the interaction forms between Hg(II) and group types (-Cl, -CN, -NH2, -OH, -COOH) in functionalized Poly(pyrrole methane)s for efficient mercury removal

To explore the impact of different functional groups on Hg(II) adsorption, a range of poly(pyrrole methane)s functionalized by -Cl, -CN, -NH2, -OH and -COOH were synthesized and applied to reveal the interaction between different functional groups and mercury ions in water, and the adsorption mechanism was revealed through combined FT-IR, XPS, and DFT calculations. The adsorption performance can be improved to varying degrees by the incorporation of functional groups. Among them, the oxygen-containing functional groups (-OH and -COOH) exhibit stronger affinity for Hg(II) and can increase the adsorption capacity from 180 mg g-1 to more than 1400 mg g-1 at 318 K, with distribution coefficient (Kd) exceeding 105 mL g-1. The variations in the capture and immobilization capabilities of functionalized poly(pyrrole methane)s predominantly stem from the unique interactions between their functional groups and mercury ions. In particular, oxygen-containing -OH and -COOH effectively capture Hg(OH)2 through hydrogen bonding, and further deprotonate to form the -O-Hg-OH and -COO-Hg-OH complexes which are more stable than those obtained from other functionalized groups. Finally, the ecological safety has been fully demonstrated through bactericidal and bacteriostatic experiments to prove the functionalized poly(pyrrole methane)s can be as an environmentally friendly adsorbent for purifying contaminated water.

A theoretical and electrochemical impedance spectroscopy study of the adsorption and sensing of selected metal ions by 4-morpholino-7-nitrobenzofuran

The selectivity of a novel chemosensor, based on a modified nitrobenzofurazan referred to as NBD-Morph, has been investigated for the detection of heavy metal cations (Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+). The ligand, 4-morpholino-7-nitrobenzofurazan (NBD-Morph), was characterized using spectroscopic techniques including FT-IR and 1H NMR. Vibrational frequencies obtained from FT-IR and proton NMR (1H) chemical shifts were accurately predicted employing the density functional theory (DFT) at the B3LYP level of theory. Furthermore, an examination of the structural, electronic, and quantum chemical properties was conducted and discussed. DFT calculations were employed to explore the complex formation ability of the NBD-Morph ligand with Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+ metal cations. The comparison of adsorption energies for all possible conformations reveals that NBD-Morph exhibits sensitivity and selectivity towards metal ions, including Pb2+, Cu2+, Ag+, and Ni2+. However, an assessment of their reactivity using QTAIM topological parameters demonstrated the ligand's greater complexation ability toward Cu2+ or Ni2+ than those formed by Pb2+ or Ag+. Additionally, molecular electrostatic potential (MEP), Hirshfeld surfaces, and their associated 2D-fingerprint plots were applied to a detailed study of the inter-molecular interactions in NBD-Morph-X (X = Pb2+, Cu2+, Ag+, Ni2+) complexes. The electron localization function (ELF) and the localized-orbital locator (LOL) were generated to investigate the charge transfer and donor-acceptor interactions within the complexes. Electrochemical analysis further corroborates the theoretical findings, supporting the prediction of NBD-Morph's sensory ability towards Ni2+ metal cations. In conclusion, NBD-Morph stands out as a promising sensor for Ni2+.

Induced mechanism of phosphatase hormesis by Cd ions and rhizosphere metabolites of Trifolium repens L

Rhizosphere phosphatases can exhibit hormetic effects in response to cadmium (Cd) ion stimulation. However, understanding the mechanisms underlying hormesis effects on soil ecosystems is challenging as studies on hormesis are usually specific to an organism, cell, or organ. To comprehensively investigate the mechanism of phosphatase hormesis, this study utilized in situ zymography and metabolomics to analyze the rhizosphere of Trifolium repens L. (white clover). Zymograms showed that rhizosphere phosphatase displayed a hormetic effect in 10 mg kg-1 Cd contaminated soil, with a hotspot area 1.8 times larger than non-Cd contaminated soil and a slight increase in enzyme activity. Nevertheless, the phosphatase activity was substantially suppressed upon elevating the Cd concentration in the soil to 50 mg kg-1. Differential metabolite identification and KEEG pathway enrichment analysis revealed that both rhizosphere organic acids and amino acid compounds positively affected phosphatase activity, and both were able to stabilize complexation with Cd ions via carboxyl groups. Besides, molecular docking models suggested that Cd ions act as cofactors to induce the formation of hydrogen bonds between amino acids/organic acids and phosphatase residues to form a triplet complex with a more stable structure, thereby improving phosphatase activity. The results indicated that amino acids and organic acids are heavily enriched in the rhizosphere of white clover and form a particular structure with soil Cd ions and phosphatase, which is essential for inducing the phosphatase hormesis as a detoxification mechanism in the rhizosphere micro-ecosystem.

Phenylarsonic acid-DMPS redox reaction and conjugation investigated by NMR spectroscopy and X-ray diffraction

The reaction between 2,3-dimercaptopropane-1-sulfonate (DMPS, unithiol) and four phenylarsonic(V) acids, i.e. phenylarsonic acid (PAA), 4-hydroxy-3-nitrophenylarsonic acid (HNPAA), 2-aminophenylarsonic acid (o-APAA) and 4-aminophenylarsonic acid (p-APAA), is investigated in aqueous solution. The pentavalent arsenic compounds are reduced by DMPS to their trivalent analogs and instantly chelated by the vicinal dithiol, forming covalent As-S bonds within a five-membered chelate ring. The different types and positions of polar substituents at the aromatic ring of the arsonic acids influence the reaction rates in the same way as observed for reaction with glutathione (GSH), as well as the syn/anti molar ratio of the diastereomeric products, which was analyzed using time- and temperature-dependent nuclear magnetic resonance (NMR) spectroscopy. Addition of DMPS to the conjugate formed by a phenylarsonic(V) acid and the biologically relevant tripeptide GSH showed the immediate replacement of GSH by chelating DMPS, underlining the importance of dithiols as detoxifying agent.

Foliar application of the sulfhydryl compound 2,3-dimercaptosuccinic acid inhibits cadmium, lead, and arsenic accumulation in rice grains by promoting heavy metal immobilization in flag leaves

Mixed pollution due to heavy metals (HMs), especially cadmium (Cd), lead (Pb), and arsenic (As), seriously endangers the safety of food produced in paddy soil. In the field experiments, foliar application of 2,3-dimercaptosuccinic acid (DMSA) at the flowering stage was found to significantly reduce the levels of Cd, Pb, total As, and inorganic As (iAs) in rice grains by 47.95%, 61.76%, 36.37%, and 51.24%, respectively, without affecting the concentration of metallonutrients, including Mn, K, Mg, Ca, Fe, and Zn. DMSA treatment significantly reduced the concentrations of Cd, Pb, and As in the panicle node, panicle neck, and rachis, while those in the flag leaves were significantly increased by up to 20.87%, 49.40%, and 32.67%, respectively. DMSA application promoted the transport of HM from roots and lower stalks to flag leaves with a maximum increase of 34.55%, 52.65%, and 46.94%, respectively, whereas inhibited the transport of HM from flag leaves to panicle, rachis, and grains. Therefore, foliar application of DMSA reduced Cd, Pb, and As accumulation in rice grains by immobilizing HMs in flag leaves. Thus, this strategy could act as a promising agronomic measure for the remediation of mixed HM contamination in paddy fields.

Synergy Effects in Heavy Metal Ion Chelation with Aryl- and Aroyl-Substituted Thiourea Derivatives

Detection and removal of metal ion contaminants have attracted great interest due to the health risks that they represent for humans and wildlife. Among the proposed compounds developed for these purposes, thiourea derivatives have been shown as quite efficient chelating agents of metal cations and have been proposed for heavy metal ion removal and for components of high-selectivity sensors. Understanding the nature of metal-ionophore activity for these compounds is thus of high relevance. We present a theoretical study on the interaction between substituted thioureas and metal cations, namely, Cd²⁺, Hg²⁺, and Pb²⁺. Two substituent groups have been chosen: 2-furoyl and m-trifluoromethylphenyl. Combining density functional theory simulations with wave function analysis techniques, we study the nature of the metal-thiourea interaction and characterize the bonding properties. Here, it is shown how the N,N'-disubstituted derivative has a strong affinity for Hg²⁺, through cation-hydrogen interactions, due to its greater oxidizing capacity.

Comparative cation sensing properties of a newly designed urea linked ferrocene-benzimidazole dyad: a DFT study

Herein, our primary motivation was to elucidate the electronic and physicochemical properties of a novel molecular dyad consisting of ferrocene (Fc; electron donor), urea (u; linker), and amphoteric benzimidazole (BI; electron acceptor) entities. The sensor responses were investigated for various divalent transition metal cations (Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺) and the selectivity of this cationophore molecule (Fc-u-BI) to copper ion (Cu²⁺) was demonstrated by using B3LYP/LANL2DZ method. According to the thermochemical calculations, we justified that Fc-u-BI⋯Cu²⁺ reached to the lowest binding energy (∆E), enthalpy (∆H), and Gibbs free energy (∆G) changes. In the light of the calculated global descriptors, Fc-u-BI⋯Cu²⁺ was found to be the softer and thus the most reactive complex. The complex stabilities and their corresponding non-covalent interactions were also investigated by NBO and NCI analyses, respectively. The mechanistic insight into metal cation sensing by the modeled cationophore dyad.

Medicinal Thiols: Current Status and New Perspectives

The thiol (-SH) functional group is found in a number of drug compounds and confers a unique combination of useful properties. Thiol-containing drugs can reduce radicals and other toxic electrophiles, restore cellular thiol pools, and form stable complexes with heavy metals such as lead, arsenic, and copper. Thus, thiols can treat a variety of conditions by serving as radical scavengers, GSH prodrugs, or metal chelators. Many of the compounds discussed here have been in use for decades, yet continued exploration of their properties has yielded new understanding in recent years, which can be used to optimize their clinical application and provide insights into the development of new treatments. The purpose of this narrative review is to highlight the biochemistry of currently used thiol drugs within the context of developments reported in the last five years. More specifically, this review focuses on thiol drugs that represent the standard of care for their associated conditions, including N-acetylcysteine, 2,3-meso-dimercaptosuccinic acid, British anti-Lewisite, D-penicillamine, amifostine, and others. Reports of novel dosing regimens, delivery strategies, and clinical applications for these compounds were examined with an eye toward emerging approaches to address a wide range of medical conditions in the future.