Inquiring 199Hg NMR Parameters by Combining Ab Initio Molecular Dynamics and Relativistic NMR Calculations

Ab initio molecular dynamics (AIMD) sampling followed by relativistic density functional theory (DFT) 199Hg NMR calculations were performed for Hg organometallic complexes in water, dimethyl sulfoxide, and chloroform. The spin-orbit coupling, a relativistic effect, is a key factor for predicting δ(Hg) and 1J(Hg-C) accurately, in conjunction with a dynamic treatment of the systems. Good agreement between the theoretical and experimental results is reached by adopting implicit (based on a continuum model) and explicit (solvent molecules treated quantum mechanically) solvation models. Broader trends appearing in the experimental data available in the literature are reproduced by the calculations, and therefore, quantum chemistry is able to assist in the assignment and interpretation of 199Hg NMR data. Less pronounced trends, such as changes in the 199Hg chemical shift in different systems with the same atom types bound to Hg, are too weak to be predicted reliably by the current state-of-the-art theoretical methods based on AIMD sampling and relativistic DFT with hybrid functionals for NMR calculations.

Novel Amperometric Mercury-Selective Sensor Based on Organic Chelator Ionophore

A novel amperometric sensor for the direct determination of toxic mercury ions, Hg²⁺, based on the organic chelator ionophore N, N di (2-hydroxy-5-[(4-nitrophenyl)diazenyl]benzaldehyde) benzene-1,2-diamine (NDBD), and multiwalled carbon nanotubes (MWCNT) immobilized on a glassy carbon electrode surface was developed. The parameters influencing sensor performance including the ionophore concentration, the applied potential, and electrolyte pH were optimized. The sensor response to Hg²⁺ was linear between 1-25 µM with a limit of detection of 60 nM. Interferences from other heavy metal ions were evaluated and the sensor showed excellent selectivity towards Hg²⁺. The method was successfully applied to the determination of mercury ions in milk and water samples.

Highly Selective MOF-Based Turn-Off Luminescence Detection of Hg2+ Ions in an Aqueous Medium and Its Dual Functional Catalytic Activity toward Aldol Condensation and β-Enamination Reactions

A new organic ligand, 5-(carboxyformamido)isophthalic acid (5-CFIA), was prepared and employed for the synthesis of two compounds [M₃(C₁₀H₄O₇N₁)₂(8H₂O)]·H₂O (M = Cd, Mn). The compounds have three-dimensionally extended structures. Both the compounds were found to be luminescent at room temperature. The luminescence nature was exploited for the detection of Hg²⁺ ions in an aqueous medium with good selectivity. The interactions between Hg²⁺ ions and the compounds quench the luminescence intensity and act as a turn-off sensor. Both the compounds exhibited low limits for the detection of Hg²⁺ ions and in the range mandated by the WHO. The interactions between Hg²⁺ ions and the compound involve the -NH group, which was probed using Raman and IR spectroscopic techniques. These studies provide important pointers toward the mechanism of this turn-off luminescence behavior. The compounds were explored for base-catalyzed aldol condensation and Lewis acid-promoted β-enaminoester formation reactions. The aldol condensation reaction uses the -NH functionality as a base. The studies indicate that the electron-withdrawing group produces products with higher yields. The β-enaminoester reaction uses the Lewis acid centers, and the studies reveal that the electron-withdrawing groups produce lesser yields of the products. The catalytic nature of the reaction and recyclability of the catalysts were also established. The catalytic reactions employ ethanol (aldol condensation) and no solvent (β-enaminoester), which suggests that the reactions are green and environmentally friendly. The Mn compound was observed to be anti-ferromagnetic.

Chemical-Shift Standards for 199Hg NMR Spectroscopy, 25 Years Later

While 199Hg NMR is a well-established tool for elucidating details of coordination chemistry in biochemical and inorganic complexes, historically the technique has been associated with the use of an extremely toxic chemical, dimethylmercury [Me2Hg or (CH3)2Hg], as a reference standard. In the 25 years since an accidental exposure to Me2Hg led to the tragic death of Dr. Karen Wetterhahn, the community has learned a great deal about the insidious neurotoxicity of this compound as well as more appropriate ways to avoid exposure. Here, we track the general shift toward the use of alternative mercury reference standards and away from Me2Hg.

Metal ion sensing with graphene quantum dots: detection of harmful contaminants and biorelevant species

Graphene quantum dots (GQDs) are attractive materials for use as highly selective and sensitive chemical sensors, owing to their simple preparation and affordability. GQDs have been successfully deployed as sensors for toxic metal ions, which is a significant issue due to the ever-increasing environmental contamination from agricultural and industrial activities. Despite the success of GQDs in this area, the mechanisms which underpin GQD-metal ion specificity are rarely explored. This lack of information can result in difficulties when attempting to replicate published procedures and can limit the judicious design of new highly selective GQD sensors. Furthermore, there is a dearth of GQD examples which selectively detect biologically relevant alkali and alkaline earth metals. This review will present the current state of GQDs as metal ion sensors for harmful contaminants, highlighting and discussing the discrepancies that exist in the proposed mechanisms regarding metal ion selectivity. The emerging field of GQD sensors for biorelevant metal ion species will also be reviewed, with a perspective to the future of this highly versatile material.

Enzymatic construction of metal-mediated nucleic acid base pairs

Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.

A portable selective electrochemical sensor amplified with Fe3O4@Au-cysteamine-thymine acetic acid as conductive mediator for determination of mercuric ion

Mercury ion (Hg²⁺) is considered to be one of the most toxic heavy metal ions and can cause adverse effects on kidney function, the central nervous system, and the immune system. Therefore, it is important to develop a fast and simple method for sensitive and selective detection of Hg²⁺ in the environment. This research proposes a portable electrochemical sensor for rapid and selective detection of Hg²⁺. The sensor platform is designed based on thymine acetic acid anchored with cysteamine-conjugated core shell Fe₃O₄@Au nanoparticles (Fe₃O₄@Au/CA/T-COOH) immobilized on a sensing area of a screen-printed carbon electrode (SPCE) with the aid of an external magnetic field embedded in a homemade electrode holder for ease of handling. In the presence of Hg²⁺, the immobilized thymine combines specifically with Hg²⁺ and forms a thymine-Hg²⁺-thymine mismatch (T-Hg²⁺-T). The resulting amount of Hg²⁺ was determined by differential pulse anodic stripping voltammetry (DPASV). Under optimal conditions, the sensor exhibited two wide linearities in a range from 1 to 200 μg L^-1 and 200-2200 μg L^-1 with the reliability coefficient of determination of 0.997 and 0.999, respectively. The detection limit (LOD) and the quantification limit (LOQ) were also determined to be 0.5 μg L^-1 and 1.0 μg L^-1, respectively. The sensor was further applied for determination of Hg²⁺ in water samples, a certified reference material and fish samples. The results were compared with flow injection atomic spectroscopy-inductively coupled plasma-optical emission spectroscopy (FIAS-ICP-OES) systems as a reference method. Results obtained with the proposed sensor were relatively satisfactory, and they showed no significant differences at a 95% confidence level by t-test from the standard method. Therefore, considering its fast and simple advantages, this novel strategy provides a potential platform for construction of a Hg²⁺ electrochemical sensor.

Bio- and Biomimetic Receptors for Electrochemical Sensing of Heavy Metal Ions

Heavy metals ions (HMI), if not properly handled, used and disposed, are a hazard for the ecosystem and pose serious risks for human health. They are counted among the most common environmental pollutants, mainly originating from anthropogenic sources, such as agricultural, industrial and/or domestic effluents, atmospheric emissions, etc. To face this issue, it is necessary not only to determine the origin, distribution and the concentration of HMI but also to rapidly (possibly in real-time) monitor their concentration levels in situ. Therefore, portable, low-cost and high performing analytical tools are urgently needed. Even though in the last decades many analytical tools and methodologies have been designed to this aim, there are still several open challenges. Compared with the traditional analytical techniques, such as atomic absorption/emission spectroscopy, inductively coupled plasma mass spectrometry and/or high-performance liquid chromatography coupled with electrochemical or UV-VIS detectors, bio- and biomimetic electrochemical sensors provide high sensitivity, selectivity and rapid responses within portable and user-friendly devices. In this review, the advances in HMI sensing in the last five years (2016-2020) are addressed. Key examples of bio and biomimetic electrochemical, impedimetric and electrochemiluminescence-based sensors for Hg2+, Cu2+, Pb2+, Cd2+, Cr6+, Zn2+ and Tl+ are described and discussed.

A review on nanostructure-based mercury (II) detection and monitoring focusing on aptamer and oligonucleotide biosensors

Heavy metal ion pollution is a severe problem in environmental protection and especially in human health due to their bioaccumulation in organisms. Mercury (II) (Hg²⁺), even at low concentrations, can lead to DNA damage and give permanent harm to the central nervous system by easily passing through biological membranes. Therefore, sensitive detection and monitoring of Hg²⁺ is of particular interest with significant specificity. In this review, aptamer-based strategies in combination with nanostructures as well as several other strategies to solve addressed problems in sensor development for Hg²⁺ are discussed in detail. In particular, the analytical performance of different aptamer and oligonucleotide-based strategies using different signal improvement approaches based on nanoparticles were compared within each strategy and in between. Although quite a number of the suggested methodologies analyzed in this review fulfills the standard requirements, further development is still needed on real sample analysis and analytical performance parameters.

QM and QM/MM umbrella sampling MD study of the formation of Hg(II)-thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

The formation of the Hg-N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg²⁺ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H₂ O)₆ ]²⁺ , (2) T + [Hg(H₂ O)₅ (OH)]⁺ , (3) T + Hg(H₂ O)₄ (OH)₂ , and (4) N3-deprotonated T + Hg(H₂ O)₄ (OH)₂ . The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4-5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg²⁺ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.

Concerted dynamics of metallo-base pairs in an A/B-form helical transition

Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-HgII-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-HgII-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-HgII-(N4)C base pairs and greater A-form characteristics. Ten-fold different 1J coupling constants (15N,199Hg) are observed for (N3)C-HgII (114 Hz) versus (N4)C-HgII (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-HgII-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding HgII, demonstrating that C-HgII-T has unique switching potential in DNA-based materials and devices.

A Novel DNA Helical Wire Containing HgII -Mediated T:T and T:G Pairs

Numerous applications of metal-mediated base pairs (metallo-base-pairs) to nucleic acid based nanodevices and genetic code expansion have been extensively studied. Many of these metallo-base-pairs are formed in DNA and RNA duplexes containing Watson-Crick base pairs. Recently, a crystal structure of a metal-DNA nanowire with an uninterrupted one-dimensional silver array was reported. We now report the crystal structure of a novel DNA helical wire containing Hg^II -mediated T:T and T:G base pairs and water-mediated C:C base pairs. The Hg-DNA wire does not contain any Watson-Crick base pairs. Crystals of the Hg-DNA wire, which is the first DNA wire structure driven by Hg^II ions, were obtained by mixing the short oligonucleotide d(TTTGC) and Hg^II ions. This study demonstrates the potential of metallo-DNA to form various structural components that can be used for functional nanodevices.

3-Fluoro-2-mercuri-6-methylaniline Nucleotide as a High-Affinity Nucleobase-Specific Hybridization Probe

A 3-fluoro-6-methylaniline nucleoside was synthesized and incorporated into an oligonucleotide, and its ability to form mercury-mediated base pairs was studied. UV melting experiments revealed increased duplex stability with thymine, guanine, and cytosine opposite to the probe and a clear nucleobase-specific binding preference (T > G > C > A). Moreover, the 3-fluoro group was utilized as a spin label that showed distinct ¹⁹F NMR resonance shifts depending on the complementary nucleobase, providing more detailed information on Hg(II)-mediated base pairing.

Metal-Mediated Base Pairs: From Characterization to Application

The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.

A review: Aptamer-based analytical strategies using the nanomaterials for environmental and human monitoring of toxic heavy metals

Recent developments in biotechnology offer the new methods for the sensitive detection of heavy metals based on the affinity and specificity of aptamers, as nucleic acid ligands selected from random sequence pools in vitro. Heavy metals have received considerable importance as the most toxic metallic pollutants which may cause serious environmental damages. They are classified as trace elements because of their presence in trace concentrations in various environmental matrices. Thus, the precise and sensitive methods to detect heavy metals are important to ensure human and environment safety. Aptamers as the biological probes, show high binding affinity which can often be directly translated into high detection sensitivity. On the other hand, high selectivity and stability make them possible to detect a wide range of targets, especially metallic ions. This review provides current progress of aptamers for environmental and biological monitoring of heavy metals using the nanomaterials mainly in two groups: (i) aptamer based biosensors (aptasensors) and (ii) aptamer based biosorbents (aptasorbents). The introduction of nanomaterials can efficiently increase the immobilization quantity of aptamers. Furthermore, they play an important role in the orientation and assembly density controlling of aptamers for the optimized recognition ability.

Self-pairing of 1-methylthymine mediated by two and three Ag(i) ions: a gas phase study using infrared dissociation spectroscopy and density functional theory

Metal base pairs comprised of silver dimer or trimer and two thymines were studied by IR dissociation spectroscopy and density functional theory.

Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs

In this feature article, recent progress and future perspectives of metal-mediated base-pairs such as T–Hg(ii)–T and C–Ag(i)–C are presented.