Investigation of the metal binding site in methionine aminopeptidase by density functional theory

All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co²⁺ions or Zn²⁺ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions. This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. colimethionine aminopeptidase type 1 (eMetAP-1). Another important structural issue is the identity of the bridging oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion.     

The effect of Fe(II) ions on the 1,10-phenanthroline and neocuproine intercalates of γ-zirconium phosphate

1,10-Phenanthroline (phen), 2,9-dimethyl-1,10-phenanthroline (neocuproine), and 4,7-dimethyl-1,10-phenanthroline have been intercalated between layers of -zirconium phosphate (-ZrP). The observed interlayer distances are not a simple function of the size of guest molecules. Despite the fact that -ZrP takes up very few Fe²⁺ ions, the phen and neocuproine intercalates do take up some Fe²⁺ ions without further changes in the interlayer distances. The chemical environments around Fe²⁺ ions between layers of the intercalates were investigated by⁵⁷Fe Mössbauer spectroscopy. A fairly large fraction of the Fe²⁺ ions was found to be in a high-spin state. The low-spin [Fe(phen)₃]²⁺ ions are also ion exchanged on -ZrP, with the expansion of the interlayer up to 19.9 Å.     

磷酸二甲酯阴离子与二价金属离子相互作用的研究

在B3LYP/6-31G(d, p)水平上,用全电子分别研究了Mg2+、Ca2+、Mn2+、Co2+、Ni2+、Cu2+和Zn2+与磷酸二甲酯(DMP-)“双齿”配位模式下的相互作用,且由4个水分子((H2O)4)“饱和”各金属离子六配位模式下的其它位点。结果表明:这种配位模式下,DMP-对上述金属离子的选择性顺序为:Cu2+>Ni2+>Zn2+>Co2+>Mg2+>Mn2+>Ca2+,和Irving-Williams序列基本一致。且具有未充满d层轨道的金属对配体的变化“响应”明显。通过NBO(自然键轨道)方法对配合物电荷布居分析可得出主族金属离子与配体间以静电相互作用为主,非主族金属离子配合物中存在一定的共价作用的结论,同时关于配合物各部分间键轨道相互作用的分析部分的反映了金属离子与配体的作用实质。     

Synthesis of lariat organochalcogenoethers based on azacalix[3]arenes for the potentiometric detection of [UO2] ions

The syntheses of organochalcogen-supported azacalix[3]arenes are described in a one-pot manner in satisfactory yields. A remarkably selective potentiometric response was accomplished for uranyl ions over a variety of other metal ions, including alkali (Na⁺, K⁺), alkaline-earth (Mg²⁺, Ca²⁺, Ba²⁺), transition and heavy metal ions (Co²⁺, Ni²⁺, Cu²⁺, Ag⁺, Fe³⁺, Zn²⁺, Cd²⁺ and Pb²⁺) using an ion-selective electrode based on compound 3 incorporated into a polymeric (PVC) membrane.     

Cation binding to biomolecules

SCF ab initio computations are carried out on the binding of alkali and alkaline-earth cations to the phosphate monoanion. The effect of the binding on the conformational properties of the phosphodiester linkage and of the polar head of phospholipids is investigated. The results indicate that following the nature of the cation and the site of its binding, the interaction may have a profound influence on the conformation of the ligand. The consequences of this situation on the use of lanthanide probes in NMR studies are considered.     

A prediction of the three-dimensional structure of maize NADP+-dependent malate dehydrogenase which explains aspects of light-dependent regulation unique to plant enzymes

Summary A model has been built for the plant NADP-malate dehydrogenase from Zea mays, a key enzyme in photosynthesis, which undergoes light-dependent regulation. The model was based on sequence and presumed structural homology to the known three-dimensional structure of mammalian porcine cytosolic NAD-malate dehydrogenase. A cystine-loop present in an extended C-terminal region of plant NADP-malate dehydrogenases was modelled using molecular mechanics and computer graphical methods, based on the assumption that a disulphide bridge exists in the inactive form of the enzyme between Cys³⁵¹ and Cys³⁶³. The predicted conformation of the intact C-terminal cystine-loop suggests that the extended polypeptide will bind in the active centre and inhibit enzyme activity. Another ionizable cysteine residue in the active site is predicted to control the charge of the catalytic His²¹⁵ and might be responsible for the uniquely tight binding of the positively charged nicotinamide ring of NADP⁺ in this and other C4 and C3 plant NADP-malate dehydrogenases.     

Free energies of transfer of alkali halides from water to urea-water mixtures at 25°C from EMF measurements

The standard potentials_s E ^o of M/M⁺ (M=Li, Na, K, Rb, and Cs) electrodes in aqueous urea solutions containing 12, 20, 30 and 37% by weight of urea have been determined at 25°C from emf measurements on the cell M(Hg)/MCl (m), solvent/AgCl–Ag, from the activities of metals in amalgams by use of a similar type of cell in water, and from the values of_s E ^o of the Ag/AgCl electrode determined earlier. The standard free energies of transfer of MCl, G _t ^o (MCl), from water to the mixed solvents, computed by use of these values and those for the Ag–AgCl electrode, rise sharply from Li⁺ to Na⁺ but fall from Na⁺ to K⁺ and rather sharply from K⁺ to Cs⁺ with a maximum at Na⁺ in all the solvent compositions. This has been attributed to the superimposition of soft-soft interactions on the electrostatic interactions between the ions and the negative charge centers of the possible hydrogen-bonded solvent complexes in the mixed solvents. Comparison of G _t ^o (i) values for individual ions, obtained by a simultaneous extrapolation procedure, with those in aqueous mixtures of methanol,t-butanol, and dimethyl sulfoxide leads to the conclusion that the solvation of these ions in all these solvents is chiefly dictated by the acid-base type of ion-solvent interactions.     

The Effect of the Spacer of Bis(biurea) Ligands on the Structure of A2L3‐type (A=anion) Phosphate Complexes

By tuning the length and rigidity of the spacer of bis(biurea) ligands L, three structural motifs of the A₂L₃ complexes (A represents anion, here orthophosphate PO₄^3?), namely helicate, mesocate, and mono‐bridged motif, have been assembled by coordination of the ligand to phosphate anion. Crystal structure analysis indicated that in the three complexes, each of the phosphate ions is coordinated by twelve hydrogen bonds from six surrounding urea groups. The anion coordination properties in solution have also been studied. The results further demonstrate the coordination behavior of phosphate ion, which shows strong tendency for coordination saturation and geometrical preference, thus allowing for the assembly of novel anion coordination‐based structures as in transition‐metal complexes.     

X-ray spectroscopic characterization of Cu2+-phenanthroline complexes intercalated in α-zirconium phosphate

X-ray photoelectron spectroscopy provides evidence that when [Cu(phen)₂]²⁺(phen = 1,10-phenanthroline) is diffused between the layers of -zirconium phosphate, the complex species does not remain intact after intercalation, but some Cu-N bonds are broken, replaced with Cu-O bonds and the released nitrogen atoms can now interact with the PO₃-OH groups of the host. XPS also provides evidence for coordination of the Cu²⁺ ions when they are diffused by ion exchange in the phenanthroline--zirconium phosphate intercalation compound. Although Cu²⁺ and phen are in a 1 : 1 molar ratio in the interlayer region of the host, so that a 1 : 1 coordination could be expected between the two species, the characteristic peaks of the uncoordinated phenanthroline, even though at a low intensity, are still present. The differences between the two Cu(II)-intercalation compounds are discussed.     

Application of 2‐(benzyliminomethyl)‐6‐methoxy‐4‐(4‐methoxyphenyl‐azo)phenol in construction of ion‐selective PVC membrane electrode for determination of copper (II) in mineral water sample

The potentiometric characteristics of a new Cu²⁺‐selective electrode based on 2‐(benzyliminomethyl)‐6‐methoxy‐4‐(4‐methoxyphenyl‐azo) phenol as an efficient ionophore has been evaluated. The effects of influential parameters on the potentiometric responses such as the amount of plasticizer, the amount of ionophore, pH of the sample solution, and the effect of coexisting ions on the electrode signal were subsequently investigated . The selectivity of the electrode was assessed by calculating the selectivity coefficients using the matched potential method. The optimum ratio of the amount of materials required for the preparation of the electrode was found to be 1.7: 32.1: 64.2: 2.0 corresponding to carboxylated PVC, dimethyl sebacate as solvent mediators, potassium tetrakis (p‐chlorophenyl) borate as the anion localizing agent, and ionophore, respectively. The electrode had a fast response (7s) as well as a satisfactory Nernstian slope (29.26±0.91 mV/decade) to Cu²⁺ over a wide concentration range of 2.0×10^?6‐ 5.0×10^?2 M with a low detection limit of 5.9×10^?7 M. The developed sensor was successfully used for the potentiometric titration of Cu²⁺ ion with EDTA and subsequently, efficient determination of this metal ion in a mineral water sample was performed.     

Crystal Structure of Two Dimethyl 1,3-Thiazolidinedicarboxylates Obtained in Thermal [2 + 3]Cycloaddition of an Azomethine Ylide with 2,2,4,4-Tetramethyl-3-Thioxocyclobutanone

The crystal structures of dimethyl 2,2,4,4-tetramethyl-3-oxocyclobutane-1-spiro-5-3,4-diphenyl-(1,3)-thiazolidine-2,2-dicarboxylate, C₂₆H₂₉NO₅S for V, and dimethyl 3,4-diphenyl-5-isopropylidene-(1,3)-thiazolidine-2,2-dicarboxylate, C₂₂H₂₃NO₄S for VI, have been solved. The 1,3-thiazolidine ring of compound V has got twisted conformation, while in compound VI this ring adopts envelope. In both structures short inter- and intramolecular contacts were found, which can be recognized as hydrogen bonds.     

Metal ion-induced FRET modulation in a bifluorophore system

A new fluorogenic sensor 1 capable of illustrating metal ion-triggered FRET changes has been synthesized. Based on the FRET changes, 1, bearing coumarin-fluorescein moieties, provides a selective sensor for Cu²⁺ and Hg²⁺ ions for experiments implemented in aqueous media with a chloride counter anion.     

Chirality Transfer in Propeller‐Shaped Cyclen?Calcium(II) Complexes: Metal‐Coordinating and Ion‐Pairing Anion Procedures

A series of quadruple‐stranded Na⁺ and Ca²⁺ complexes with octadentate cyclen ligands was synthesized to produce complexes that contained four different side‐arm combinations (one triazole? coumarin group and three pyridine groups ( 1 ), four pyridine groups ( 2 ), one triazole? coumarin group and three quinoline groups ( 3 ), and four quinoline groups ( 4 )). X‐ray crystallographic analysis revealed that no significant changes occurred in the stereostructure of these complexes upon replacing one pyridine group with a triazole? coumarin moiety, or by replacing Na⁺ ions with Ca²⁺ ions, although the coordination number of the complexes in the solid state decreased when pyridine groups were replaced by quinoline groups. In solution, all of the side arms were arranged in a propeller‐like pattern to yield an enantiomer pair of Δ and Λ forms in each metal complex. The addition of a tert‐butoxycarbonyl (Boc)‐protected amino acid anion, that is, a coordinative chiral carboxylate anion, to the cyclen? Ca²⁺ complex induced circular dichroism (CD) signals in the aromatic region by forming a 1:1 mixture of diastereomeric ternary complexes with opposite complex chirality, whilst the corresponding Na⁺ complexes rarely showed any response. In complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺, this chirality‐transfer process was efficiently followed by considering the induction of the CD signals at two different wavelengths, that is, the coumarin‐chromophore region and the aza‐aromatic region. The sign and intensity of the CD signal were significantly dependent on both the nature of the aza‐aromatic moiety and the enantiomeric purity of the external anion. These Ca²⁺ complexes worked as effective probes for the determination of the enantiomeric excess of the chiral anion. The cyclen? Ca²⁺ complexes also interacted with the non‐coordinative Δ‐TRISPHAT anion through an ion‐pairing mechanism to achieve chirality transfer from the anion to the metal complex; both complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺ clearly showed induced CD signals in the coumarin‐chromophore region, owing to ion‐paring interactions with the Δ‐TRISPHAT anion. Thus, the proper combination of an octadentate cyclen ligand and a metal center demonstrated effective chirality transfer.     

Potentiometric and Thermodynamic Studies of 5-(4′-Sulfonylazidophenylazo)-3-phenyl-2-thioxothiazolidin-4-one and Its Metal Complexes

The proton dissociation constant of 5-(4-sulfonylazidophenylazo)-3-phenyl-2-thio- xothiazolidin-4-one (SPT) and the stability constants of its complexes with some metal ions were calculated potentiometrically in 0.1 M KCl and 40% (v/v) ethanol–water mixture. The order of stability was found to be Mn²⁺ < Co²⁺ < Ni²⁺ < Cu²⁺ < Zn²⁺. The effect of temperature on the dissociation of SPT and the stability of its complexes were studied. The corresponding thermodynamic functions were derived and discussed. The dissociation process is unspontaneous, endothermic, and entropically unfavorable. The formation of the metal complexes was found to be spontaneous, endothermic and entropically favorable.     

Colloidal copper in aqueous solutions: radiation-chemical reduction,mechanism of formation,and properties

Colloidal copper has been obtained by -irradiation of aqueous solutions of copper (II) perchlorate in the presence of alcohol and polyethyleneimine (PEI). The sols are spherical particles about 4 nm in diameter, which are quickly oxidized by oxygen or other oxidants. When Cu^II is not entirely incorporated into the complex with PEI, disproportionation of Cu^I aqua complexes formed affords the metal, along with Cu₂O. Reduction of the PEI complex of Cu^I by hydrated electrons gives only colloidal copper. The copper ions can be reduced on the surface of silver sols. Optical parameters of the resulting bimetallic particles have been studied. The presence of copper ions leads to broadening of the absorption band associated with the silver sols and shifts it to the UV region, which is due to the transfer of electrons from copper to silver. Three copper monolayers are enough to cause plasmon absorption of colloidal copper.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 25–30, January, 1994.     

Preparation of a Novel Agarose-Salen Adsorbent,and its Use for Efficient Column Preconcentration and Flame AAS Determination of Lead in Water

A cross-linked agarose (Novarose) support was chemically modified with a novel salen-type Schiffs base; 2,2-[1,2-ethandiyl bis(nitrilimethylidyne)] bis(orthocresol) and was used to develop an efficient, simple and low-cost method for matrix separation and preconcentration of lead in water. The binding capacity of the adsorbent, packed in a 6.5mm i.d. glass column, was tested for different metal ions, and a capacity of 4973 (±95) µg per mL of packed adsorbent for triplicate measurements was obtained for lead at pH 6.0.The effects of pH, ionic strength, buffer concentration, sample volume, eluent concentration and volume, and matrix ions on the column recovery of Pb²⁺ were carefully studied. Quantitative recoveries were obtained for the analyte in a pH range of 5.5 to 7.0. Enrichment volumes up to 300mL and ionic strengths up to 0.5molL^–1 had no significant effect on the recovery of Pb²⁺. The method also tolerated relatively high concentrations of matrix ions such as Ca²⁺, Mg²⁺, Fe³⁺, Cu²⁺, Zn²⁺, Mg²⁺ and Cd²⁺ with no considerable effect on the analytes signal. A few mL of 0.4molL^–1 hydrochloric acid was sufficient for quantitative elution of the analyte from a 0.5mL column before its flame AAS determination. Preconcentration factors up to 60 and a detection limit of 2.5µgL^–1 were obtained for the method. The precision, expressed as relative standard deviation, was 2.9% (at 100µgL^–1) calculated from six replicate measurements. The method was successfully applied to the determination of Pb²⁺ in some river and spiked river water samples with good precision.     

Synthesis of γ-zirconium phosphate by the fluoro-complex method and the intercalation behavior of some α-diimines

The ammonium form of -zirconium phosphate has been synthesized by the direct precipitation method from fluorozirconate solution in the presence of ammonium dihydrogen phosphate. The hydrogen form Zr(HPO₄)₂ · 2H₂O, was obtained by acid treatment of the ammonium form -Zirconium phosphate , Zr(HPO₄)₂ · H₂O, with a relatively large particle size resulted from fluorozirconate solution in the presence of concentrated orthophosphoric acid. The intercalation behavior of such -diimines as 2,2-bipyridine (bpy) and 1,10-phenanthroline (phen) toward -zirconium phosphate was investigated, and it was found that about 0.2 mol of bpy and 0.5 mol of phen have been incorporated respectively per one mol of the host, with the expansion of interlayer distances. Further incorporation of Cu(H) ions into the interlayer space of these intercalates was possible. The bpy intercalate took up more Cu(II) ions than -zirconium phosphate, indicating that effective pillars are constructed between layers and the ion exchange of Cu(II) ions is facilitated thereby.     

Quantum chemical studies on electrophilic addition

The geometries of the 2-hydroxyethyl and isomeric oxiranium cations have been fully optimized using ab initio molecular orbital calculations employing the split valence shell 4-31G basis set. These species are possible intermediates in both the electrophilic addition of OH to ethylene and in the acid catalysed ring opening of oxirane. The optimized structures were then used to compute more accurate wave functions using Dunning's double-zeta basis set, and with this large basis set the bridged oxiranium ion was found to be the more stable by 7.2 kcal/mole. The barrier to interconversion of these two C₂H₄OH ions was computed to be 25.0 kcal/mole above the oxiranium ion.     

Free energies of transfer of alkali metal halides in isodielectric acetonitrile and ethylene glycol mixtures at 25°C

Standard free energies of transfer (G _t ^o ) of alkali metal chlorides MCl (M=Li, Na, K, Rb, Cs) and of potassium bromide and iodide from ethylene glycol to its isodielectric mixtures containing 20, 40, and 60 wt. % acetonitrile have been determined from emf measurements at 25°C. The standard potentials of the M/M⁺, the Ag–AgBr, and the Ag–AgI electrodes have been calculated using auxiliary emf measurements. All electrolytes were found to be increasingly destabilized in mixed solvents of increasing acetonitrile content; the relative order of cation destabilization is Li⁺>Na⁺>K⁺>Rb⁺>Cs⁺ and that of anion destabilization is Cl^–>Br^–>I^–, both following (a) the order of increasing softness of ions and increasing interaction with the soft base, acetonitrile,and (b) the order of decreasing hydrogen-bonding propensity of ions and decreasing interactions with the hard base, ethylene glycol.