Theoretical Study of Hydrated Copper(II) Interactions with Guanine: A Computational Density Functional Theory Study

Micron-Scale Fabrication of Ultrathin Amorphous Copper Nanosheets Templated by DNA Scaffolds

Two-dimensional (2D) amorphous materials could outperform their crystalline counterparts toward various applications because they have more defects and reactive sites and thus could exhibit a unique surface chemical state and provide an advanced electron/ion transport path. Nevertheless, it is challenging to fabricate ultrathin and large-sized 2D amorphous metallic nanomaterials in a mild and controllable manner due to the strong metallic bonds between metal atoms. Here, we reported a simple yet fast (10 min) DNA nanosheet (DNS)-templated method to synthesize micron-scale amorphous copper nanosheets (CuNSs) with a thickness of 1.9 ± 0.4 nm in aqueous solution at room temperature. We demonstrated the amorphous feature of the DNS/CuNSs by transmission electron microscopy (TEM) and X-ray diffraction (XRD). Interestingly, we found that they could transform to crystalline forms under continuous electron beam irradiation. Of note, the amorphous DNS/CuNSs exhibited much stronger photoemission (∼62-fold) and photostability than dsDNA-templated discrete Cu nanoclusters due to the elevation of both the conduction band (CB) and valence band (VB). Such ultrathin amorphous DNS/CuNSs hold great potential for practical applications in biosensing, nanodevices, and photodevices.

Highly selective removal of Ni(II) from plating rinsing wastewaters containing [Ni-xNH3-yP2O7]n complexes using N-chelating resins

Inorganic complexants, such as ammonia (AA) and pyrophosphate (PP), are often present alongside heavy metal ions in alkaline plating rinsing wastewater. We investigated the removal capacity of Ni(II) from waters containing [Ni-xNH₃-yP₂O₇]ⁿ complexes by chelating and ion-exchange resins in sole and dual-ligand systems. D463 (containing iminodiacetic groups) and PAMD (possessing polyamine groups) exerted superior performance under all conditions. Ni(II) adsorption on D463 decreased with AA and PP by 10.3% and 64.4%, respectively. Conversely, the adsorption on PAMD increased by 57.3% and 75.8%, respectively. PAMD exhibited high selectivity toward anionic [Ni-PP] species over free PP. More Ni(II) was captured by PAMD in the dual-ligand systems than sole systems, while the case for D463 was opposite. As confirmed by species tracking and DFT/XPS analyses, complexes breaking-Ni²⁺ capture was the dominant mechanism for D463, while the dual-site (non-charged and protonated amines) interactions with NiP₂O₇^2- on PAMD promoted its adsorption. The tandem combination D463-PAMD was the optimal mode to remove the most Ni(II). The actual wastewater test demonstrated that >210 BV effluent met the limit of 0.1 mg Ni(II)/L and the eluent contained 15 g Ni(II)/L. This study guides the application of chelating adsorption processes in the advanced treatment of plating rinsing wastewaters.

Molecular Facts on the Structure and Dynamics of Electrolyte Species in Cu-Cl Cycle for Hydrogen Generation: An Insight from Molecular Dynamic Simulations

The Cu complex, which is the key chemical species in well-known Cu-Cl hybrid thermochemical cycles and also in numerous metal hydrometallurgical and sedimentary deposit processes, displays a wide variety of structural and dynamical characteristics that are further complicated by the presence of multiple oxidation states of Cu ions with different coordination chemistries, therefore they are difficult to explore from experiments alone. In this article, an attempt has been made to understand the coordination behavior of the Cu complex using MD simulations. The study provides compelling evidence of the experimentally observed multiple stoichiometries of Cu ions, i.e., 1:6:0, 1:5:1, and 1:4:2 for Cu⁺:H₂O:Cl^- and 1:6:0 for Cu²⁺:H₂O:Cl^-. The presence of the anionic Cu complex, [Cu⁺Cl₂]^-·2H₂O, [Cu⁺Cl₂]^-·3H₂O, [Cu²⁺Cl₃]^-·H₂O, and [Cu²⁺Cl₃]^-·2H₂O, was captured in the presence of excess chloride ions. Furthermore, the probability distribution profiles have been estimated to determine the most possible complex in the considered systems. The results establish structural and dynamical reformation of the Cu complex with change in the salt concentration or variation in the solvent medium in which they are dissolved. Moreover, the structure and kinetics of the Cu ions in the Cu-Cl electrolyzer have been explored over a large range of the electric field by extending the simulated systems for varied strengths of the electric fields. It has been observed that with an increase in the strength of the electric field, the water molecules lose their coordination strength with central Cu ions, which, on the other hand, results in a significant change in the structure of the captured complex. The diffusion dynamics of the ions is altered while applying the electric field, which is furthermore modified while increasing the strength of electric field beyond a critical limit. In fact, the diffusion mechanism of the ions was seen to be transformed from Brownian-like to linear motion and then to hopping diffusion with the increasing strength of the electric field. To the best of our knowledge, this is the first time when the multiple oxidation states of the Cu ion are explored using MD simulations, and the coexisting pictures of the multiple coordinations and the solvent effects have been clearly revealed. Also to date, the present article is the first one to report the insights of the structure and the dynamics of the ions in the Cu-Cl electrolyzer over a wide range of the electric field. The present studies will be very helpful in understanding the mechanism involved in numerous metal hydrometallurgical and sedimentary deposit processes and to comprehend the analogies involved in the electrode reactions of the Cu-Cl cycle for hydrogen generation.

The effect of electrostatic boundaries in molecular simulations: symmetry matters

Artifacts arise when the long-ranged electrostatic interaction is inappropriately treated in molecular simulations of electrolytes. When the usual Ewald3D sum method with the tinfoil boundary condition (e3dtf) is used for simulations of an interfacial liquid under an external electric field, a straightforward analysis of the liquid structure often suggests unphysical dielectric properties as a consequence of the inaccurate treatment of the electrostatics. In order to understand the underlying mechanism that leads to this apparent violation of thermodynamics, we now derive a new equation in the weak-field limit that, in a mean field view, accounts for the average effect arising from the difference between e3dtf and the sophisticated Ewald2D sum method (e2d). Numerical simulations of a water system in slab geometry confirm the validity of the weak-field limit equation for a series of parameter setup associated with e3dtf. Moreover, a similar procedure applied to a spherically confined water system suggests that corrections to the seemingly inappropriate treatment of the electrostatics in fact vanish. This cancellation of the boundary effect due to symmetry immediately sheds light on the long-lasting problem of the validity of the ad hoc application of e3dtf for bulk systems. In total, we argue that artifacts arising from e3dtf are often predictable and analytical corrections to the straightforward analysis might be applied to reveal consistent thermodynamic properties in liquid simulations.

Insight into selective removal of copper from high-concentration nickel solutions with XPS and DFT: New technique to prepare 5N-nickel with chelating resin

An efficient and profitable separation process was proposed to prepare 5N (the purity of the metal solution reaches 99.999%) high-purity nickel from 3N nickel-solutions using Purolite S984. The adsorption performance of this superior resin, especially its selectivity for metal ions, was explored quantitatively. The maximum adsorption capacity for copper was 2.286mmol/g calculated by the Langmuir model, which was twice as large as that for nickel. In the binary systems, the adsorption capacity for nickel was decreased by 45%, indicating direct competition for the active sites. The infinite separation factor for copper versus nickel exceeded 300, revealing the feasibility of preparing 5N-level high-purity nickel solutions, which was further verified using the 800BV (bed volume) effluent in the column dynamic process. According to the cost-benefit analysis, purification contributed to a profit of approximately 60,000USD per cycle, and the investment return period was less than 1/3years. Density functional theory analysis confirmed that four nitrogen atoms would be involved in the coordination complex and thus a structure involving two five-membered rings could be achieved. The X-ray photoelectron spectra confirmed the involvement of nitrogen atoms, implying a coordination ratio of approximately 1:1.

Metal-mediated DNA damage and cell death: mechanisms, detection methods, and cellular consequences

Metal ions cause various types of DNA damage by multiple mechanisms, and this damage is a primary cause of cell death and disease.

Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations

B3LYP density functional based computations were performed in order to characterize the interactions present in some Cu(+), Ag(+), and Au(+) metal ion-mediated DNA and RNA base pairs from both structural and electronic points of view. Examined systems involve as ligands canonical Watson-Crick, Hoogsteen and Wobble base pairs. Two artificial Hoogsteen base pairs were also taken into account. Binding energy values indicate that complexes involving silver cations are less stable than those in which copper or gold are present, and propose a similar behaviour for these two latter ions. The nature of the bond linking metal ions and bases was described by the NBO analysis that suggests metal coordinative interactions to be covalent. An evaluation of the dispersion contributions for the investigated systems was performed with the B3LYP-D3 functional.

Selective electroless deposition of copper on organic thin films with improved morphology

We have investigated the selective electroless deposition (ELD) of Cu on functionalized self-assembled monolayers (SAMs). Previous studies have demonstrated that Cu deposits on -COOH and -CH(3) terminated SAMs using ELD. However, the deposited films were rough and contained irregular crystallites. Further, the copper penetrated through the film. In this Article, we demonstrate that copper can be selectively deposited on -COOH terminated SAMs with improved morphology and without penetration of copper through the organic layer. The method employs a Cu(II) seed layer and an additive, adenine or guanine. We demonstrate the efficacy of the technique on photopatterned -CH(3)/-COOH SAMs. Copper is observed to deposit only atop the -COOH terminated SAM area and not on the -CH(3) terminated SAM. The use of a Cu(II) seed layer increased the Cu ELD rate on both -COOH and -CH(3) terminated SAMs. The deposited copper layer strongly adheres to the -COOH terminated SAMs because the copper layer nucleates at Cu(2+)-carboxylate complexes. In contrast, the deposited copper layer can easily be removed from the -CH(3) terminated SAM surface because there is no specific copper-surface interaction. The additives adenine and guanine mediate the interaction of Cu(2+) and the deprotonated -COOH terminated SAMs via the formation of additive-carboxylate complexes. These complexes lead to significantly reduced copper penetration through the SAM. In the case of adenine, the diffusion of copper through the organic film was eliminated. This new technique for copper deposition will facilitate the development of inexpensive molecular electronics, sensors, and other nanotechological devices.

Quantum-chemical study of interactions of trans-resveratrol with guanine-thymine dinucleotide and DNA-nucleobases

Trans-resveratrol, a natural phytoalexin present in red wine and grapes, has gained considerable attention because of its antiproliferative, chemopreventive and proapoptotic activity against human cancer cells. The accurate quantum-chemical computations based on the density functional theory (DFT) and ab initio second-order Møller-Plesset perturbation method (MP2) have been performed for the first time to study interactions of trans-resveratrol with guanine-thymine dinucleotide and DNA-derived nitrogenous bases: adenine, guanine, cytosine and thymine in vacuum and water medium. This compound is found to show high affinity to nitrogenous bases and guanine-thymine dinucleotide. The electrostatic interactions from intermolecular hydrogen bonding increase the stability of complexes studied. In particular, significantly strong hydrogen bonds between 4'-H atom of trans-resveratrol and imidazole nitrogen as well as carbonyl oxygen atoms of nucleobases studied stabilize these systems. The stabilization energies computed reveal that the negatively charged trans-resveratrol-dinucleotide complex is more energetically stable in water medium than in vacuum. MP2 method gives more reliable and significantly high values of stabilization energy of trans-resveratrol-dinucleotide, trans-resveratrol-guanine and trans-resveratrol-thymine complexes than B3LYP exchange-correlation functional because it takes into account London dispersion energy. According to the results, in the presence of trans-resveratrol the 3'-5' phosphodiester bond in dinucleotide can be cleaved and the proton from 4'-OH group of trans-resveratrol migrates to the 3'-O atom of dinucleotide. It is concluded that trans-resveratrol is able to break the DNA strand. Hence, the findings obtained help understand antiproliferative and anticancer properties of this polyphenol.

Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: experimental and theoretical study

Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+) cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm(-1) band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region ( approximately 800-1200 cm(-1)), but also notable frequency shifts of the carbonyl vibrations. The Cu(2+) and Zn(2+) ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu(2+) binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids.