AM1* parameters for manganese and iron

We report the parameterization of AM1* for the elements manganese and iron. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, I and Au. The performance and typical errors of AM1* are discussed for Mn and Fe, and are compared with available NDDO Hamiltonians.     

AM1* parameters for gold

We report the parameterisation of AM1* for gold. The basis set for gold contains one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, I and Au. The performance and typical errors of AM1* for gold are discussed.     

AM1* parameters for palladium and silver

We report the parameterization of AM1* for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, Ag, I and Au. The performance and typical errors of AM1* are discussed for Pd and Ag and compared with the PM6 Hamiltonian.     

AM1* parameters for vanadium and chromium

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements V and Cr. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Cu, Zn, Br, Zr, Mo and I. The performance and typical errors of AM1* are discussed for V and Cr and compared with available NDDO Hamiltonians. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

AM1* parameters for copper and zinc

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Cu and Zn. The basis sets for both metals contain a set of d-orbitals. The zinc parameterization uses a filled d-shell to give 12 valence electrons. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Cu, Zn, Zr and Mo. The performance and typical errors of AM1* are discussed for the newly parameterized elements. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

AM1* parameters for bromine and iodine

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Br and I. The basis sets for both halogens contain a set of d-orbitals as polarization functions. AM1* performs as well as other MNDO-like methods that use d-orbitals in the basis, and better than those that rely on an sp-basis. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Cu, Zn, Br, Zr, Mo and I. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

AM1* parameters for aluminum, silicon, titanium and zirconium

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Al, Si, Ti and Zr. The basis sets for all four metals contain a set of d-orbitals. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Mo and Zr. Special attention was paid to reproducing homolytic and heterolytic bond-dissociation energies correctly. Such bond-energy data help to avoid eccentricities in the parameterization caused by inaccurate experimental heats of formation. The performance and typical errors of AM1* for the newly parameterized elements are discussed. Generally, the new method performs less well than established techniques for heats of formation but considerably better for the heats of reaction. Electronic Supplementary Material Supplementary material is available for this article at     

AM1* parameters for phosphorus,sulfur and chlorine

An extension of the AM1 semiempirical molecular orbital technique, AM1*, is introduced. AM1* uses AM1 parameters and theory unchanged for the elements H, C, N, O and F. The elements P, S and Cl have been reparameterized using an additional set of d orbitals in the basis set and with two-center core–core parameters, rather than the Gaussian functions used to modify the core–core potential in AM1. Voityuk and Röschs AM1(d) parameters have been adopted unchanged for AM1* with the exception that new core–core parameters are defined for Mo–P, Mo–S and Mo–Cl interactions. Thus, AM1* gives identical results to AM1 for compounds with only H, C, N, O, and F, AM1(d) for compounds containing Mo, H, C, N, O and F only, but differs for molybdenum compounds containing P, S or Cl. The performance and typical errors of AM1* are discussed.Electronic Supplementary Material Supplementary material is available in the online version of this article at . Tables 2 and 4–7 and a full list (Tables S1, S2) of geometrical parameters and barrier heights are given in the supplementary material.This revised version was published online in September 2003.     

Spectroscopic characterization of metal binding by Klebsiella aerogenes UreE urease accessory protein

 The urease accessory protein encoded by ureE from Klebsiella aerogenes is proposed to function in Ni(II) delivery to the urease apoprotein. Wild-type UreE contains a histidine-rich region at its carboxyl terminus and binds 5–6 Ni per dimer, whereas the functionally active but truncated H144*UreE lacks the histidine-rich motif and binds only two Ni per dimer [Brayman TG, Hausinger RP (1996) J Bacteriol 178 : 5410-5416]. For both proteins, Cu(II), Co(II), and Zn(II) ions compete for the Ni-binding sites. In order to characterize the coordination environments of bound metals, especially features that are unique to Ni, the Ni-, Cu-, and Co-bound forms of H144*UreE were studied by a combination of EPR, ESEEM, hyperfine-shifted ¹H-NMR, XAS, and RR spectroscopic methods. For each metal ion, the two binding sites per homodimer were spectroscopically distinguishable. For example, the two Ni-binding sites each have pseudo-octahedral geometry in an N/O coordination environment, but differ in their number of histidine donors. The two Cu-binding sites have tetragonal geometry with two histidine donors each; however, the second Cu ion is bound by at least one cysteine donor in addition to the N/O-type donors found for the first Cu ion. Two Co ions are bound to H144*UreE in pseudo-octahedral geometry with N/O coordination, but the sites differ in the number of histidine donors that can be observed by NMR. The differences in coordination for each type of metal ion are relevant to the proposed function of UreE to selectively facilitate Ni insertion into urease in vivo. Received: 8 October 1997 / Accepted: 30 December 1997     

Nickel remediation by AM-colonized sunflower

This greenhouse study aimed to examine the contribution of arbuscular mycorrhizal (AM) colonization on the uptake of and tolerance to nickel (Ni) in sunflower (Helianthus annuus L.). We hypothesized that AM colonization increases Ni content and tolerance in sunflower grown under varying soil Ni concentrations. The combined effect of AM colonization and soil Ni input on the assimilation of nitrogen, in particular the activity of glutamine synthetase (GS), in sunflower plants was also investigated. A factorial experimental design was performed with sunflower cv. Lemon Queen, with or without the AM fungus, Glomus intraradices Schenck & Smith, and treated with 0, 100, 200, or 400 mg Ni kg⁻¹ dry soil (DS). The AM colonization significantly enhanced plant growth and Ni content, especially at the lower soil Ni treatments. Furthermore, the AM plants exposed to the highest soil Ni level of 400 mg Ni kg⁻¹ DS had a significantly higher shoot Ni extracted percentage than non-AM plants, suggesting that the AM symbiosis contributed to Ni uptake, then its translocation from roots to shoots. The AM colonization also significantly increased the GS activity in roots, this being likely an indicator of an enhanced Ni tolerance. These findings support the hypothesis that AM symbiosis contributes to an enhanced Ni plant uptake and tolerance and should be considered as part of phytoremediation strategies.     

Chemiluminescence assay for Listeria monocytogenes based on Cu/Co/Ni ternary nanocatalyst coupled with penicillin as generic capturing agent

Bacterial pathogen control is important in seafood production. In this study, a Cu/Co/Ni ternary nanoalloy (Cu/Co/Ni TNA) was synthesized using the oleylamine reducing method. It was found that Cu/Co/Ni TNA greatly enhanced the chemiluminescence (CL) signal of the hydroxylamine‐O‐sulfonic acid (HOSA)–luminol system. The CL properties of Cu/Co/Ni TNA were investigated systemically. The possible CL mechanism also was intensively investigated. Based on the enhanced CL phenomenon of Cu/Co/Ni TNA, a Cu/Co/Ni TNA, penicillin, and anti‐L. monocytogenes (Listeria monocytogenes) antibody‐based sandwich complex assay for detection of L. monocytogenes was established. In this sandwich CL assay, penicillin was employed to capture and enrich pathogenic bacteria with penicillin‐binding proteins (PBPs) while anti‐L. monocytogenes antibody was adopted as the specific recognition molecule to recognize L. monocytogenes. L. monocytogenes was detected sensitively based on this new Cu/Co/Ni TNA–HOSA–luminol CL system. The CL intensity was proportional to the L. monocytogenes concentration ranging from 2.0 × 10² CFU ml^?1 to 3.0 × 10⁷ CFU ml^?1 and the limit of detection wa 70 CFU ml^?1. The reliability and potential applications of our method was verified by comparison with official methods and recovery tests in environment and food samples.     

Multipole electrostatic potential derived atomic charges in NDDO-methods with <Emphasis Type="Italic">spd</Emphasis>-basis sets

The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159–168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol⁻¹, respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively. Figure: Schematic representation of the atomic charge generation: The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian; then the semiempirical MEP is scaled to DFT or ab initio level, and atomic charges are generated subsequently by the restraint electrostatic potential (RESP) fit method. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible to authorized users. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

Applicability of Heavy-Metal Phytoextraction in United Arab Emirates: An Investigation of Candidate Species

Phytoremediation of contaminated calcareous desert land in the United Arab Emirates has been investigated. Soils from 12 northern UAE sites, suspected of metal contamination, were acid-extracted and analyzed by ICP-OES for Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn. Twenty-two plants naturally growing at contaminated sites were sampled and analyzed for their uptake of Co, Cr, Cu, Mn, Ni, Pb, and Zn and eight commercially available plants, grown under controlled conditions, were also studied for their phytoextraction capabilities. The concentration of available Cr was found to be 1300 ± 150 mg/kg in the soil of the Ajman Industrial Zone and 80 ± 10 mg/kg of Pb was found at Bithna. Among the plants investigated, Portulaca oleracea and Iresine herbstii showed potential for Cr(VI) and Pb(II) accumulation, respectively, with bioconcentration factors (BCF) greater than unity. Atriplex halimus accumulated Co(II), Cr(III), and Cu(II) each with a BCF > 1.     

Nickel tolerance and accumulation by bacteria from rhizosphere of nickel hyperaccumulators in serpentine soil ecosystem of Andaman, India

Rhizosphere microorganisms harboring nickel hyperaccumulators, Rinorea bengalensis (Wall.) O. K. and Dichapetalum gelonioides ssp. andamanicum (King) Leenh. endemic to serpentine outcrops of Andaman Islands, India, were screened for their tolerance and accumulation of Ni. The rhizosphere soils from both the plants were rich in total and available Ni along with Co, Cr, Fe and Mg but poor in microbial density and were dominated by bacteria. Out of total 123 rhizosphere microorganisms (99 bacteria and 24 fungi), bacteria were more tolerant to Ni than fungi. Viable cells of selected Ni-tolerant bacterial isolates (MIC = 13.6–28.9 mM Ni) belonging to Pseudomonas, Bacillus and Cupriavidus were capable of accumulating nickel (209.5–224.0 μM Ni g⁻¹ protein) from aqueous solution. Cupriavidus pauculus KPS 201 (MTCC 6280), showing highest degree of nickel tolerance (MIC 28.9 mM Ni) and uptake (224.0 μM Ni g⁻¹ protein, 60 min) was used for detailed study. Kinetics of nickel uptake in C. pauculus KPS 201 followed a linearized Lineweaver-Burk plot. The K _m and V _max for nickel uptake by minimal medium grown-cells approximated 1.5 mM Ni and 636.9 μM Ni g⁻¹ protein, respectively. The uptake process was inhibited by Co, Cu, Cd, Mg, Mn and Zn, however, complete inhibition was not achieved even in presence of 500 mM Mg. Metabolic inhibitors, sodium azide (1.0 mM) and carbonyl cyanide m-chlorophenylhydrazone (0.4 mM) strongly inhibited nickel uptake suggesting the process as an energy dependent one. The present study clearly shows that bacteria in the rhizosphere of Ni-hyperaccumulators are capable of tolerating high concentration of Ni and also possesses nickel uptake potential. The Ni-hyperaccumulators in combination with these Ni-resistant bacteria could be an ideal tool for nickel bioremediation.     

Bivalent Metal Chelates with Pentadentate Azo-Schiff Base Derived from Nicotinic Hydrazide: Preparation,Structural Elucidation,and Pharmacological Activity

Azo-Schiff base ligand (N′-((E)-2-hydroxy-5-((E)-(2-hydroxyphenyl)diazenyl)benzylidene)nicotinohydrazide) and its Mn(II), Co(II), Ni(II), Cu(II), Zn(II) and Pd(II) chelates were prepared and elucidated. The geometrical structures of the prepared chelates were characterized by several spectroanalytical techniques and thermogravimetric analysis. The obtained data revealed that the chelates have (1M:1L), (1M:2L), (1M:3L), and (1M:4L) molar ratios. The infrared spectra displayed that the H₂L ligand behaves in a pentacoordinate fashion in chelates of Mn(II), Ni(II), and Cu(II) ions. However, in Zn(II) and Pd(II) chelates, the ligand is coordinated as a tetradentate species (NONO) through nitrogen atoms of azomethine and azo groups as well as oxygen atoms of phenolic hydroxy, and carbonyl groups. Besides, it was concluded that the oxygen atoms of carbonyl and hydroxy groups along with the azomethine nitrogen atom of the ligand are bounded with Co(II) ion in metal chelate ( 2 ). According to the measured molar conductance values, the chelates of Cu(II), Zn(II), and Pd(II) are weak electrolytes, but Mn(II), Co(II), and Ni(II) chelates are ionic. The azo-Schiff base ligand and its prepared metal chelates were tested for their antioxidant and antibacterial properties. The Ni(II) chelate was found to be considered an effective antioxidant agent. In addition, the available antibacterial data suggest that the Ni(II) and Co(II) chelates may be employed as inhibitor agents against Proteus vulgaris, Escherichia coli, and Bacillus subtilis bacteria. Furthermore, the data showed that, in comparison to the ligand and other metal chelates, copper(II) chelate (4) exhibited higher action against Bacillus subtilis bacteria.     

Phytoextraction of Soil Cobalt Using Hyperaccumulator Plants

A greenhouse study was conducted on phytoextraction of cobalt by nickel hyperaccumulators Alyssum murale and Alyssum corsicum and by two varieties of cobalt accumulator Nyssa sylvatica compared with the nonmetal accumulator crop plant Brassica juncea. The plants were grown on Sassafras sandy loam soil (<2 mg Co and 5 mg Ni/kg dry soil), amended with 1 mmol Co/kg dry soil (58.9 mg/kg), and two Ni smelter-contaminated soils, Quarry muck with 24 mg Co and 1720 mg Ni/kg dry soil and Welland loam with 37 mg Co and 2570 mg Ni/kg dry soil. All soils were adjusted to pH 6.5 to prevent Ni phytotoxicity. Of the five plant entries tested in the study, the two Alyssum species demonstrated the most promising Co phytoextraction results. In Co-amended Sassafras soil, the maximum concentration accumulated by Alyssum murale was 1320 mg Co/kg dry weight, which was almost 60 times higher than accumulation by crop plant Brassica juncea. At a single harvest after 60 days of growth, A. murale was able to extract more than 3% of Co from Co-amended soil. As expected, both Alyssum species accumulated up to 1% Ni on dry weight basis when grown on Ni-contaminated soils.

Nyssa sylvatica showed considerable Co accumulation; foliar Co concentration in the second harvest was as high as 800 mg/kg dry weight. The first few leaves that emerged were chlorotic, both in the Co-amended soil and Ni-contaminated soils, but with growth the signs of toxicity disappeared. In the Co amended soil, Co concentration in Nyssa sylvatica leaves was 30% of that found in shoots of Alyssum species, but an order of magnitude higher than that of Brassica juncea. The leaves accumulated a higher concentration compared with the stems.

Both Alyssum species and Nyssa sylvatica offer promise for phytoextraction of Co and ⁶⁰Co from contaminated or mineralized soils.     

Comparative studies of nickel,cobalt, and copper uptake by some nickel hyperaccumulators of the genus Alyssum

The uptake of Ni, Co, and Cu by the nickel hyperaccumulator Alyssum troodii Boiss and the non-accumulator Aurinia saxatilis (L.) Desv. were studied in pot trials using artificial rooting media with varying concentrations of the metals added as soluble salts, singly and in combination. The ability of five other Ni hyperaccumulating species of Alyssum to hyperaccumulate Co was also investigated.Leaves and stems of A. troodii accumulated Ni to almost the same extent (8000–10 000 g g^-1). In roots, the highest Ni concentration was 2000 g g^-1. In leaves of Au. saxatilis, the maximum Ni concentration was only 380 g g^-1 and the level in roots was even lower.In media containing Co, the maximum concentration of this element in A. troodii (2325 g g^-1) was ten times higher than in the non-accumulator species. Slightly less Co was found in stems and roots of both species. Among the other Ni hyperaccumulators, the maximum concentration of Co in leaves ranged from about 1000–8000 g g^-1.Copper concentrations were the same in all organs of both species when they were grown in copper-rich media and were in the range 40–80 g g^-1, showing that neither plant was capable of taking up Cu at levels comparable to those of Ni and Co.When both plants were grown in media containing equal amounts of both Co and Ni, the Co concentrations in plant organs were the same as for specimens grown in media containing Co only. However, the Ni levels were lower in both species. Uptake of Co therefore appeared to suppress Ni uptake.Pot trials showed that the order of tolerance was Ni>Cu>Co for A. troodii and Ni>CoCu for Au. saxatilis, whereas the seedling tests showed the order to be Co>Ni>Cu. At metal concentrations 10 000 g g^-1, the overall tolerance of A. troodii was greater than that of Au. saxatilis which exhibited equally low tolerance to Ni and Cu.We conclude that in A. troodii, A. corsicum Duby, A. heldreichii Hausskn., A. murale Waldstein & Kitaibel, A. pintodasilvae T.R. Dudley, and A. tenium Hálácsy, Ni tolerance and hyperaccumulation conveys the same character towards Co. This behaviour should be investigated in other hyperaccumulators of Ni and/or Co.     

Complexes of vitamin B6, part VII: Ternary complexes of cobalt(II), nickel(II), and copper(II) involving pyridoxamine and some amino acids

The stability constants of the ternary Cu(II), Ni(II), and Co(II) complexes containing pyridoxamine (PM) and as a second ligand (L) glycine, DL-alanine, DL-valine, and β-phenylalnine were determined by pH-metric titration in 0.50 M KNO₃ at 30°C. The corresponding constants of the equilibrium, log X, are greater than would be expected for purely statistical reasons (log X = 0.6), except for few complex cases of Co(II). It has been also concluded that amino acids compete more than pyridoxamine for Ni(II) and Co(II) through the formation of 1:2:1:0 species rather than 2:1:1:0 of PM⁻:L⁻:M²⁺:H⁺.     

Ectomycorrhizal and arbuscular mycorrhizal colonization of Alnus acuminata from Calilegua National Park (Argentina)

The objective of this study was to determine patterns of ectomycorrhizas (ECM) and arbuscular mycorrhizas (AM) colonization associated with Alnus acuminata (Andean alder), in relation to soil parameters (electrical conductivity, field H₂O holding capacity, pH, available P, organic matter, and total N) at two different seasons (autumn and spring). The study was conducted in natural forests of A. acuminata situated in Calilegua National Park (Jujuy, Argentina). Nine ECM morphotypes were found on A. acuminata roots. The ECM colonization was affected by seasonality and associated positively with field H₂O holding capacity, pH, and total N and negatively associated with organic matter. Two morphotypes (Russula alnijorullensis and Tomentella sp. 3) showed significant differences between seasons. Positive and negative correlations were found between five morphotypes (Alnirhiza silkacea, Lactarius omphaliformis, Tomentella sp. 1, Tomentella sp. 3, and Lactarius sp.) and soil parameters (total N, pH, and P). A significant negative correlation was found between field H₂O holding capacity and organic matter with AM colonization. Results of this study provide evidence that ECM and AM colonization of A. acuminata can be affected by some soil chemical edaphic parameters and indicate that some ECM morphotypes are sensitive to changes in seasonality and soil parameters.     

In Situ Probing and Synthetic Control of Cationic Ordering in Ni‐Rich Layered Oxide Cathodes

Ni‐rich layered oxides (LiNi_1–x M_x O₂; M = Co, Mn, …) are appealing alternatives to conventional LiCoO₂ as cathodes in Li‐ion batteries for automobile and other large‐scale applications due to their high theoretical capacity and low cost. However, preparing stoichiometric LiNi_1–x M_x O₂ with ordered layer structure and high reversible capacity, has proven difficult due to cation mixing in octahedral sites. Herein, in situ studies of synthesis reactions and the associated structural ordering in preparing LiNiO₂ and the Co‐substituted variant, LiNi_0.8Co_0.2O₂, are made, to gain insights into synthetic control of the structure and electrochemical properties of Ni‐rich layered oxides. Results from this study indicate a direct transformation of the intermediate from the rock salt structure into hexagonal phase, and during the process, Co substitution facilities the nucleation of a Co‐rich layered phase at low temperatures and subsequent growth and stabilization of solid solution Li(Ni, Co)O₂ upon further heat treatment. Optimal conditions are identified from the in situ studies and utilized to obtain stoichiometric LiNi_0.8Co_0.2O₂ that exhibits high capacity (up to 200 mA h g^?1 ) with excellent retention. The findings shed light on designing high performance Ni‐rich layered oxide cathodes through synthetic control of the structural ordering in the materials.