Metal Ion Ligand Research Articles

New insights in the bonding regime and ligand field in Wernerian complexes. A density functional study

We advance challenging new observations about the bonding regime and ligand field (LF) effects in the Wernerian complexes, with the help of several computer experiments realized exploiting the specific leverages of the ADF (Amsterdam density functional) code. Assembling the molecular systems from preliminarily prepared metal ion and individual ligand fragments and analyzing the components of the total bonding energy (Pauli repulsion, electrostatic interactions and orbital part), we noticed interesting correlations between the orbital part and the simple formulas of the qualitatively defined ligand field stabilization energy (LFSE). The facts are beyond the obvious or predictable comprehension, since the orbital components incorporate the subtle balance of intra- and inter-fragment density rearrangements, charge transfer and orbital mixing. The energy decomposition analysis was performed considering metal ions and ligand sets in their nominal oxidation states, or with fractional charges, resulted after a preliminary step of electronegativity equalization driven charge transfer. We worked on series of prototypic simple octahedral units: [MqF6]q−6 , [Mq(CN)6]q−6 and [Mq(H2O)6]q complexes with MII and MIII ions selected from the M=Cr to Cu 3d series. Besides, as illustration of observed regularities in the case of more complex ligands and intermediate symmetries, we considered [Mq(bpca)2]q−2 complexes (Hbpca=bis(2-pyridilcarbonyl)amine) with D2d symmetry. Using the ADF facilities of orbital population control and fractional occupation schemes, we devised two simple ways to estimate 10Dq parameters by numerical experiments that simulate the effects of Ligand Field stabilization and electron promotion. To the best of our knowledge, though simple, such considerations on bonding regime or methodological procedures designed to meet the phenomenological demands of LF models have not been discussed before. Interesting new aspects can yet be discovered exploring the subtle details of coordination bonding as intermediate between ionic and covalent bonding regime.

Biological inorganic chemistry: a new introduction to molecular structure and function

Biological Inorganic Chemistry: A New Introduction to Molecular Structure and Function, Second Edition, provides a comprehensive discussion of the biochemical aspects of metals in living systems. Beginning with an overview of metals and selected nonmetals in biology, the book then discusses the following concepts: basic coordination chemistry for biologists; structural and molecular biology for chemists; biological ligands for metal ions; intermediary metabolism and bioenergetics; and methods to study metals in biological systems. The book also covers metal assimilation pathways; transport, storage, and homeostasis of metal ions; sodium and potassium channels and pumps; magnesium phosphate metabolism and photoreceptors; calcium and cellular signaling; the catalytic role of several classes of mononuclear zinc enzymes; the biological chemistry of iron; and copper chemistry and biochemistry. In addition, the book discusses nickel and cobalt enzymes; manganese chemistry and biochemistry; molybdenum, tungsten, vanadium, and chromium; non-metals in biology; biomineralization; metals in the brain; metals and neurodegeneration; metals in medicine and metals as drugs; and metals in the environment. * Winner of a 2013 Textbook Excellence Awards (Texty) from the Text and Academic Authors Association* Readable style, complemented by anecdotes and footnotes* Enables the reader to more readily grasp the biological and clinical relevance of the subject* Color illustrations enable easy visualization of molecular mechanisms

Organic Chemistry of DNA Functionalization; Chromophores as DNA Base Substitutes versus DNA Base/2′-Modifications

Nucleic acids are suitable scaffolds for the precise arrangement of different kinds of artificial functionalities inside or along the double helix. In this account, we summarize our synthetic efforts over the last ten years to modify DNA chemically with organic chromophores, fluorescent probes, and metal-ion ligands. We used three different approaches: (i) replacement of DNA bases (substitutes/surrogates), (ii) modifications of DNA bases (mainly 2′-deoxyuridine), and (iii) sugar modifications at the 2′-position. The first two types of modifications were achieved mainly by the DNA building block approach, whereas the latter type is based on postsynthetic methodologies. The different synthetic concepts are described and the influence of representative modifications on the melting temperature is compared.

Specific Binding of Anionic Porphyrin and Phthalocyanine to the G-Quadruplex with a Variety of in Vitro and in Vivo Applications

The G-quadruplex, a four-stranded DNA structure with stacked guanine tetrads (G-quartets), has recently been attracting attention because of its critical roles in vitro and in vivo. In particular, the G-quadruplex functions as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplex can show peroxidase-like activity with an anionic porphyrin, iron (III) protoporphyrin IX (hemin). Importantly, hemin binds to G-quadruplexes with high selectivity over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), which is attributable to an electrostatic repulsion of phosphate groups in ssDNA and dsDNA. The G-quadruplex and hemin-G-quadruplex complex allow development of sensing techniques to detect DNA, metal ions and proteins. In addition to hemin, anionic phthalocyanines also bind to the G-quadruplex formed by human telomere DNA, specifically over ssDNA and dsDNA. Since the binding of anionic phthalocyanines to the G-quadruplex causes an inhibition of telomerase activity, which plays a role in the immortal growth of cancer cells, anionic phthalocyanines are promising as novel anticancer drug candidates. This review focuses on the specific binding of hemin and anionic phthalocyanines to G-quadruplexes and the applications in vitro and in vivo of this binding property.

Synthesis, Spectral Study and Biological Activity of Some Metal Ions Complexes with Bidentate Ligands

A new neutral bidentate schiff base mixed ligand metal ions complexes of the composition, [ML 1 L] (NO3)2 where M=Co(II), Ni(II), Cu(II), Zn(II) and Cd (II) L 1 =(4-nitro benzylidene)-urea amine, L=L a ,L b ligands derived from thiosemicarbazone and 4-chlorobenzaldehyde or 4bromobenzaldehyde were synthesis and characterized by elemental analysis, magnetic susceptibility, molar conductivity, FT-IR, UV-Vis, and 1 HNMR spectral studies .The conductivity measurements of cobalt(II), nickel (II),and copper (II) complexes were suggested to have a tetrahedral geometry, but Zn(II) and Cd (II) complexes were suggested to has square planner. The structural geometries of compounds were also suggested in gas phase by theoretical treatments, using Hyper chem-6 program for the molecular mechanics and semi-empirical calculations, an addition heat of formation (∆Hf ◦ ) and binding energy (∆Eb) for the free ligands and it’s metal complexes were calculated by using PM3 method .PM3 was used to evaluate the vibration spectra of Schiff bases and compare the theoretically calculated wave numbers with experimental values ,the theoretically obtained frequencies agreed calculation helped to assign unambiguously the most diagnostic bands. The antimicrobial activities of the metal chelats against the bacteria, Escherichia coli and Staphylococcus aureus were studied.

Construction of Metal–Organic Frameworks Based on Two Neutral Tetradentate Ligands

The solvothermal reaction of two new neutral tetradentate ligands with different bivalent metal salts gave seven metal–organic frameworks (MOFs): [Co2(L1) (trans-chdc)2]·5H2O (1), [Zn2(L1)(trans-chdc)(NO2)2]·DMF (2), [Cd2(L1)(trans-chdc)2]·4H2O (3), [Zn2(L1)(1,4-bdc)2]·(H2O)3 (4), [Cd2(L1)(1,4-bdc)2]·DMF·(solvent)x (5), [Co(L2) (trans-chdc)(H2O)]·1.5H2O (6), [Co(L2) (1,4-bdc) (H2O)] · 2H2O (7), (L1 = 1,1′-oxybis[3,5-diimidazole]-benzene, L2 = 1,1′-oxybis[3,5-dipyridine]-benzene, trans-chdc = trans-1,4-cyclohexanedicarboxylic acid, 1,4-bdc = 1,4-benzenedicarboxylate). These MOFs were prepared to examine the effects of the core metal ion or organic ligand on the topology and interpenetration form. The results show that the imidazole ligand can rotate easily to coordinate to metal ions, while pyridine ligand exhibits the weaker coordinative abilities, which may influence the self-assembly. Compounds 1, 3, and 5 are three-dimensional (3D) frameworks with 2-fold interpenetrated forms, whereas complex 4 shows a...

Effect of fulvic acid on neodymium uptake by goethite

Experimental studies of the interaction of aqueous neodymium (Nd), Suwannee River fulvic acid (FA), and solid phase goethite were conducted. Results from blank systems (individual Nd and FA), binary systems (Nd–goethite, FA–goethite, and Nd–FA), and ternary systems (Nd–FA–goethite) at 0.1mol/kg and 25°C are reported.In the binary Nd–goethite system a classic sorption edge is observed, whereby virtually all Nd is removed from solution above the goethite point of zero charge (PZC). Similarly, the binary FA–goethite system exhibits strong FA sorption; However in this system near complete removal of FA from solution is observed below the goethite PZC. In the binary Nd–FA system, both aqueous Nd and FA feature a sharp decrease in concentration at ca. pH 9.Various experiments in the ternary system were conducted. For all concentrations, FA enhanced Nd sorption below the goethite PZC, attributed to the formation of a Type B ternary surface complex (mineral–ligand–metal ion). Notably, the 100ppm FA ternary system showed anomalously high dissolved Nd in solution above the PZC (i.e., Nd sorption suppression) and a concomitant increase in goethite dissolution (∼9ppm total Fe3+ observed above circa pH 9.5).Our results suggest that Nd–FA complexation plays a key role in Nd uptake by goethite, and that this process is largely governed by pH: Whereas at pHs below the goethite PZC, Nd–FA complexation facilitates Nd sorption, above the PZC, and particularly at elevated FA concentrations, the formation of aqueous Nd–FA complexes suppresses Nd removal. Moreover, under these conditions, goethite dissolution may also play a role in mitigating Nd uptake by goethite.

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

The linear interaction energy (LIE) method to compute binding free energies is applied to lectin-monosaccharide complexes. Here, we calculate the binding free energies of monosaccharides to the Ralstonia solanacearum lectin (RSL) and the Pseudomonas aeruginosa lectin-II (PA-IIL). The standard LIE model performs very well for RSL, whereas the PA-IIL system, where ligand binding involves two calcium ions, presents a major challenge. To overcome this, we explore a new variant of the LIE model, where ligand-metal ion interactions are scaled separately. This model also predicts the saccharide binding preference of PA-IIL on mutation of the receptor, which may be useful for protein engineering of lectins.

L-Aspartic acid/L-cysteine/gold nanoparticle modified microelectrode for simultaneous detection of copper and lead

This paper presents an electrochemical microsensor for simultaneous detection of copper (II) and lead (II) using an l-aspartic acid/l-cysteine/gold nanoparticle modified microelectrode. The microelectrode was fabricated by Micro Electro-Mechanical System technique. The complex of gold nanoparticles (AuNPs) and amino acid with carboxyl group was used as the selective ligand for metal ions. The microelectrode was firstly modified with AuNPs to increase the sensitive area of the working electrode. Subsequently, the AuNPs/gold electrode was modified with l-cysteine and then covalently linked with a monolayer of l-aspartic acid using glutaraldehyde. Electrochemical analysis of metal ions was achieved by using square wave voltammetry without stirring. The microsensor exhibited an excellent linear range from 5μgL−1 to 2000μgL−1 with the limit of detection of 1μgL−1. This metal ion detection method based on l-aspartic acid/l-cysteine/gold nanoparticle modified microelectrode is simple, sensitive and it could be used for electrochemical analysis of copper (II) and lead (II).

Experimental and Theoretical Evidence for Encapsulation and Tethering of 1,10-Phenanthroline Complexes of Fe, Cu, and Zn in Zeolite–Y

Tris(1,10-phenanthroline) complexes of iron(II), copper(II), and zinc(II) have been encapsulated within the supercage of zeolite–NaY by the reaction of exchanged metal ion and flexible ligand that diffuses into the cavities. The hybrid material obtained has been characterized by elemental analysis (EDX), SEM, powder XRD, FTIR, UV–vis/DRS, cyclic voltammetry, and EPR techniques. The Fe and Cu complexes show electrochemical behavior in the presence of 0.1 M TBAP, whereas Zn complex gives electrochemical response only in the presence of H+ ion. This difference in electrochemical behavior of the complexes indicates an intrazeolite electron transport in the case of Fe and Cu phenanthroline complexes and an extrazeolite electron transport in the case of Zn complex anchored on the surface of zeolite–Y. The red shifting of UV–vis spectra and changes in redox properties of intrazeolite complexes in comparison to those of the neat complexes suggest that the zeolite matrix influences the electronic properties. This ...

Synthesis and structure of expanded pyriporphyrins containing a dipyrrylpyridine unit

Expanded pyriporphyrins with five and ten nitrogens were prepared in 67% and 6.5% yield, respectively, by the reactions of bis(azafulvene) and dipyrrylpyridine. The minimum 17-membered non-aromatic macrocycle made of four pyrroles and one pyridine is highly non-planar in comparison with orangarin that contains a tripyrrole unit instead of a dipyrrylpyridine unit. This highly non-planar ring structure is basically unchanged in the complex with trifluoroacetic acid (TFA) where carboxylate anions are bound on both sides of the macrocyle plane by multiple hydrogen bondings. This monopyridine-tetrapyrrole hybrid macrocycle was able to act as a dianionic ligand for various metal ions including lanthanide ions. In contrast to the reported figure eight type X-ray structure of turcasarin that is a double sized macrocycle of orangarin, the pyridine-containing macrocycle analog of the same 34-membered ring size isolated in this study was found not to take a figure eight type conformation as evidenced by X-ray crystallography of the tetracation with TFA anions.

Role of the N-terminus in determining metal-specific responses in the E. coli Ni- and Co-responsive metalloregulator, RcnR.

RcnR (resistance to cobalt and nickel regulator) is a 40-kDa homotetrameric protein and metalloregulator that controls the transcription of the Co(II) and Ni(II) exporter, RcnAB, by binding to DNA as an apoprotein and releasing DNA in response to specifically binding Co(II) and Ni(II) ions. Using X-ray absorption spectroscopy (XAS) to examine the structure of metals bound and lacZ reporter assays of the transcription of RcnA in response to metal binding, in WT and mutant proteins, the roles of coordination number, ligand selection, and residues in the N-terminus of the protein were examined as determinants in metal ion recognition. The studies show that the cognate metal ions, Co(II) and Ni(II), which bind in (N/O)(5)S six-coordinate sites, are distinguished from non-cognate metal ions (Cu(I) and Zn(II)), which bind only three protein ligands and one anion from the buffer, by coordination number and ligand selection. Using mutations of residues near the N-terminus, the N-terminal amine is shown to be a ligand of the cognate metal ions that is missing in the complexes with non-cognate metal ions. The side chain of His3 is also shown to play an important role in distinguishing metal ions. The imidazole group is shown to be a ligand in the Co(II) RcnR complex, but not in the Zn(II) complex. Further, His3 does not appear to bind to Ni(II), providing a structural basis for the differential regulation of RcnAB by the two cognate ions. The Zn(II) complexes change coordination number in response to the residue in position three. In H3C-RcnR, the Zn(II) complex is five-coordinate, and in H3E-RcnR the Zn(II) ion is bound to six protein ligands. The metric parameters of this unusual Zn(II) structure resemble those of the WT-Ni(II) complex, and the mutant protein is able to regulate expression of RcnAB in response to binding the non-cognate ion. The results are discussed within a protein allosteric model for gene regulation by metalloregulators.

An efficient and facile synthesis of polydentate ligand: pyridylpyrimidine-2-amine under solvent-free conditions

An efficient and facile synthesis of polydentate ligand pyridylpyrimidine-2-amine via a one-pot reaction of different aromatic aldehydes, 2-acetylpyridine and guanidine carbonate, in the presence of NaOH under solvent-free conditions, is reported. These compounds have four N-donors and they are classic polydentate ligands of many metal ions. Due to employing a one-pot, multicomponent reaction, this method offers several advantages including easy experimental work-up procedure, and lower cost, short reaction time, and especially high yields of products. This paper therefore develops a practical and convenient process for the synthesis of these ligands.

On-line chiral analysis of benzylmercapturic acid and phenylmercapturic acid in human urine using UPLC-QToF mass spectrometry with the kinetic method

A novel analytical method was developed for chiral analysis utilizing on-line ultra-performance liquid chromatography (UPLC) coupled with a quadrupole time-of-flight mass spectrometry (QToF-MS). This developed method was applied to discriminate and quantify accurately the chiral biomarkers, d/l-phenylmercapturic acid (PMA) and d/l-benzylmercapturic acid (BMA), in urine samples. Initially, UPLC was used to separate achirally the mixture of two biomarkers and then sequential on-line mass spectrometry differentiated successfully the enantiomers of each biomarker. After separating the two molecular species, a mixture of metal ion and reference ligand was added to the eluent of UPLC to produce trimeric M(II)-bound complex ion, [MII(A)(ref*)2-H]+ (MII, divalent transition metal ion; A, analyte; ref*, reference ligand). The collision-induced dissociation (CID) of the trimeric complex ion resulted in two dimeric complex ions, [MII(A)(ref*)-H]+ and [MII(ref*)2-H]+. The ratio of the abundances for the two product ions, the branching ratio, was established for one enantiomer relative to the other, which affects chiral discrimination. The compounds, Cu(II) as a central metal ion and L-Pro as a reference ligand were selected for the optimum distinction of chiral PMA and BMA. Rapid quantitative chiral analysis of PMA and BMA was achieved by constructing calibration curves derived from the kinetic method, related to the ratio of the branching ratios against the enantiomeric composition of their mixture.

Medium Dependent Dual Turn-On/Turn-Off Fluorescence System for Heavy Metal Ions Sensing

A dual turn-on/turn-off fluorescence sensing system based on N-alkylaminopyrazole ligands for heavy metal ions, where the response can be tuned upon medium change, is developed. The synthesis and characterization of ZnII, CdII and HgII complexes with two N-alkylaminopyrazole ligands, used as metal receptors, are first presented. The acidity and complexation constants for a selected ligand (1-[2-(octylamino)ethyl]-3,5-diphenylpyrazole ligand (L2)) with ZnII, CdII, and HgII are also determined. The fluorescent behavior of these complexes can be tuned by the different medium used (e.g., MeOH or HCl) giving rise to two different sensing mechanisms. The L2 ligand can be applied as a global heavy metal warning chemosensor (for PbII, ZnII, CdII, or HgII ions) for water samples achieving detection limits lower than the maximum concentration recommended by the environmental agencies (detection limit lower than 0.3 ng/mL for any of the mentioned metal ions). The utility of the developed sensing system for HgII dete...

有機化学反応からみた化学発光：過シュウ酸エステル化学発光を中心とした基礎的研究および応用展開

Chemiluminescence is a phenomenon in which an electronically excited fluorescent molecule is generated during the chemical reaction and emits light as a visual output. Although there have been numerous investigations of chemiluminescence so far, a lot of problems unsettled are remaining, for example, a question of what is the high-energy intermediates that interact with fluorophores. In this review, our investigations on chemiluminescence from the viewpoint of organic chemistry are described, emphasizing the mechanistic studies and the application of peroxyoxalate chemiluminescence. Employing various reactive oxalate derivatives, the kinetic studies allowed us to suggest the structures of the high-energy intermediates in the peroxyoxalate chemiluminescence. The chemiluminescence of the suitable phosphonate carbanions during the oxy-Wittig type reaction was also mentioned, in which the phospha-1,2-dioxetane is the most likely high-energy intermediate. Some chemiluminescence reactions were connected with ligand-metal ion host-guest chemistry to get a useful hint for further application of chemiluminescence to chemical detection.

Designing of ligands for solvent extraction of Cs+using molecular modeling approach

Abstract A molecular modelling (MM) approach has been adopted for designing new ligands for the extraction of Cs+. The structures of the metal ion-ligand complexes were initially optimized using FORCITE molecular mechanics module of Materials Studio 3.2. The ab initio DMol3 DFT calculations were further conducted on the MM optimized structures. The selectivity of designed ligands for Cs+ was ascertained by interaction, strain and hydration energies.

Complexation and sorption studies of Co(II) with γ-alumina-bound fulvic acid: effect of pH, ionic strength, fulvic acid and alumina concentration

The removal of heavy metal ion Co(II) from aqueous solution is studied using c-Al2O3 by batch tech- nique. The experiments are performed at T = 20 ± 2 C, in 0.01 M NaNO3 solutions and under aerobic conditions. The effect of pH, ionic strength, fulvic acid (FA) and alumina concentration on the sorption of Co(II) on alumina are also respectively investigated. The pH affects the sorption of Co(II) significantly as compared with the effect of FA and ionic strength. The results indicate that strong chemical bonds are formed between Co(II) and the bare or FA coated alumina surface, and a transition from the adsorption to surface-induced precipitation of Co(II) on alumina surface takes place. The addition sequences of Co/ FA on Co(II) sorption is also studied and the results indi- cate that the sorption of Co(II) in ternary system is inde- pendent of addition sequences. The results also suggest that the sorption of metal ions on mineral surface depends on the nature of mineral, nature of organic ligand and nature of metal ion.

MINAS—a database of Metal Ions in Nucleic AcidS

Correctly folded into the respective native 3D structure, RNA and DNA are responsible for uncountable key functions in any viable organism. In order to exert their function, metal ion cofactors are closely involved in folding, structure formation and, e.g. in ribozymes, also the catalytic mechanism. The database MINAS, Metal Ions in Nucleic AcidS (http://www.minas.uzh.ch), compiles the detailed information on innersphere, outersphere and larger coordination environment of >70 000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 Å radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids.

Rcl1 Protein, a Novel Nuclease for 18 S Ribosomal RNA Production

In all forms of life, rRNAs for the small and large ribosomal subunit are co-transcribed as a single transcript. Although this ensures the equimolar production of rRNAs, it requires the endonucleolytic separation of pre-rRNAs to initiate rRNA production. In yeast, processing of the primary transcript encoding 18 S, 5.8 S, and 25 S rRNAs has been studied extensively. Nevertheless, most nucleases remain to be identified. Here, we show that Rcl1, conserved in all eukaryotes, cleaves pre-rRNA at so-called site A(2), a co-transcriptional cleavage step that separates rRNAs destined for the small and large subunit. Recombinant Rcl1 cleaves pre-rRNA mimics at site A(2) in a reaction that is sensitive to nearby RNA mutations that inhibit cleavage in vivo. Furthermore, mutations in Rcl1 disrupt rRNA processing at site A(2) in vivo and in vitro. Together, these results demonstrate that the role of Rcl1 in eukaryotic pre-rRNA processing is identical to that of RNase III in bacteria: to co-transcriptionally separate the pre-rRNAs destined for the small and large subunit. Furthermore, because Rcl1 has no homology to other known endonucleases, these data also establish a novel class of nucleases.