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 cobalt and nickel

We report the parameterization of AM1* for the elements Co and Ni. 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, Co, Ni, Cu, Zn, Br, Zr, Mo and I. The performance and typical errors of AM1* are discussed for Co and Ni and compared with available NDDO Hamiltonians.     

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.     

Effects of mycorrhizal fungus isolates on mineral acquisition by Panicum virgatum in acidic soil

 Plant ability to withstand acidic soil mineral deficiencies and toxicities can be enhanced by root-arbuscular mycorrhizal fungus (AMF) symbioses. The AMF benefits to plants may be attributed to enhanced plant acquisition of mineral nutrients essential to plant growth and restricted acquisition of toxic elements. Switchgrass (Panicum virgatum L.) was grown in pH_Ca (soil:10 mM CaCl₂, 1 : 1) 4 and 5 soil (Typic Hapludult) inoculated with Glomus clarum, G. diaphanum, G. etunicatum, G. intraradices, Gigaspora albida, Gi. margarita, Gi. rosea, and Acaulospora morrowiae to determine differences among AMF isolates for mineral acquisition. Shoots of mycorrhizal (AM) plants had 6.2-fold P concentration differences when grown in pH_Ca 4 soil and 2.9-fold in pH_Ca 5 soil. Acquisition trends for the other mineral nutrients essential for plant growth were similar for AM plants grown in pH_Ca 4 and 5 soil, and differences among AMF isolates were generally higher for plants grown in pH_Ca 4 than in pH_Ca 5 soil. Both declines and increases in shoot concentrations of N, S, K, Ca, Mg, Zn, Cu, and Mn relative to nonmycorrhizal (nonAM) plants were noted for many AM plants. Differences among AM plants for N and Mg concentrations were relatively small (<2-fold) and were large (2- to 9-fold) for the other minerals. Shoot concentrations of mineral nutrients did not relate well to dry matter produced or to percentage root colonization. Except for Mn and one AMF isolate, shoot concentrations of Mn, Fe, B, and Al in AM plants were lower than in nonAM plants, and differences among AM plants for these minerals ranged from a low of 1.8-fold for Fe to as high as 6.9-fold for Mn. Some AMF isolates were effective in overcoming acidic soil mineral deficiency and toxicity problems that commonly occur with plants grown in acidic soil. Accepted: 14 June 1999     

Direct and Mn-Controlled Indirect Iron Oxidation by Leptothrix discophora SS-1 and Leptothrix cholodnii

Direct biotic and homogeneous abiotic Fe(II) oxidation rates as well as oxidation rates of Fe(II) with MnO_X were determined in laboratory experiments and compared with biotic Mn(II) oxidation rates. In groundwaters and thermal installation waters, parameters for both Fe(II) oxidation steps were studied and products of biotic and abiotic Fe(II) and Mn(II) oxidation were analyzed. Direct Fe(II) oxidation of active Leptothrix cholodnii cultures can reach first-order rates of up to 1.17 ± 0.90 h^?1. Second-order rates of Fe(II) oxidation with biogenic, Leptothrix-cholodnii- and Leptothrix-discophora-SS-1-originating MnO_X lead to rates comparable with those as obtained with abiotic H⁺-birnessite.     

Genetic evidence that induction of root Fe(III) chelate reductase activity is necessary for iron uptake under iron deficiency†

Reduction of Fe(III) to Fe(II) by Fe(III) chelate reductase is thought to be an obligatory step in iron uptake as well as the primary factor in making iron available for absorption by all plants except grasses. Fe(III) chelate reductase has also been suggested to play a more general role in the regulation of cation absorption. In order to experimentally address the importance of Fe(III) chelate reductase activity in the mineral nutrition of plants, three Arabidopsis thaliana mutants (frd1-1, frd1-2 and frd1-3), that do not show induction of Fe(III) chelate reductase activity under iron-deficient growth conditions, have been isolated and characterized. These mutants are still capable of acidifying the rhizosphere under iron-deficiency and accumulate more Zn and Mn in their shoots relative to wild-type plants regardless of iron status. frd1 mutants do not translocate radiolabeled iron to the shoots when roots are presented with a tightly chelated form of Fe(III). These results: (1) confirm that iron must be reduced before it can be transported, (2) show that Fe(III) reduction can be uncoupled from proton release, the other major iron-deficiency response, and (3) demonstrate that Fe(III) chelate reductase activity per se is not necessarily responsible for accumulation of cations previously observed in pea and tomato mutants with constitutively high levels of Fe(III) chelate reductase activity.     

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.     

秦艽药材及其生长土壤中无机元素含量特征及相关性分析

该研究采用原子吸收分光光度法和火焰光度法,测定云南20个种植地的秦艽及其生长土壤中无机元素的含量,探讨药材中无机元素分布特征,并对药材中无机元素含量与土壤中无机元素含量的相关性进行了分析。结果表明：云南秦艽药材无机元素的含量呈现K>Ca>Mg>Fe>Mn>Zn>Cu有规律的分布态势;通过相关性分析、主成分分析和逐步回归分析发现秦艽的特征元素为K、Cu、Ca和Zn;药材中钾含量与土壤中锌,钙与土壤中锰和铜,锰与土壤中钙和镁,铜与土壤中钾和锌元素含量间均分别显著负相关;而药材中镁含量与土壤中钙和镁,铁、铜与土壤中铁元素含量间均呈显著正相关。对秦艽各无机元素含量影响最大的因子是秦艽生长土壤有效钙,有效铁和有效锌其次,最后为有效锰。该研究结果为秦艽道地性成因及适宜栽培区域的选择提供了参考,为秦艽资源合理利用和GAP研究以及从无机元素的角度品评药材品质提供了理论依据。     

Overexpression of METAL TOLERANCE PROTEIN8 reveals new aspects of metal transport in Arabidopsis thaliana seeds

• METAL TOLERANCE PROTEIN8 (MTP8) of Arabidopsis thaliana is a member of the CATION DIFFUSION FACILITATOR (CDF) family of proteins that transports primarily manganese (Mn), but also iron (Fe). MTP8 mediates Mn allocation to specific cell types in the developing embryo, and Fe re-allocation as well as Mn tolerance during imbibition. We analysed if an overexpression of MTP8 driven by the CaMV 35S promoter has an effect on Mn tolerance during imbibition and on Mn and Fe storage in seeds, which would render it a biofortification target.
• Fe, Mn and Zn concentrations in MTP8-overexpressing lines in wild type and vit1-1 backgrounds were analysed by ICP-MS. Distribution of metals in intact seeds was determined by synchrotron µXRF tomography.
• MTP8 overexpression led to a strongly increased Mn tolerance of seeds during imbibition, supporting its effectiveness in loading excess Mn into the vacuole. In mature seeds, MTP8 overexpression did not cause a consistent increase in Mn and Fe accumulation, and it did not change the allocation pattern of these metals. Zn concentrations were consistently increased in bulk samples.
• The results demonstrate that Mn and Fe allocation is not determined primarily by the MTP8 expression pattern, suggesting either a cell type-specific provision of metals for vacuolar sequestration by upstream transport processes, or the determination of MTP8 activity by post-translational regulation.

     

Arbuscular mycorrhizal (AM) technology for the conservation of <Emphasis Type="Italic">Curculigo orchioides</Emphasis> Gaertn.: an endangered medicinal herb

Curculigo orchioides Gaertn. (family Hypoxidaceae) is an endangered anticarcinogenic and aphrodisiac herb, native of India. This study reports the effect of three arbuscular mycorrhizal (AM) fungal inocula on post-transplanting performance of ‘in vitro’ raised C. orchioides plantlets. The three AM fungal inocula consisted of two monospecific cultures of Glomus geosporum and G. microcarpum and one crude consortium of AM fungal spores isolated from rhizosphere soil of C. orchioides growing in natural habitat. Complete plantlets of C. orchioides were raised by direct organogenesis of leaf explants on half strength Murashige and Skoog’s medium devoid of any growth hormone. C. orchioides plantlets responded significantly different to all three mycorrhizal treatments. Mycorrhization enhanced the survival rate of C. orchioides plantlets to 100%. The inoculated plantlets fared significantly better than the uninoculated ones in terms of biomass production and number of leaves and roots per plant. Mycorrhizal plantlets exhibited higher concentrations of photosynthetic pigments as well as minerals P, Mg, Cu, Zn, Mn and Fe in both shoots and roots. Among the three inocula tested, plantlets inoculated with the mixed consortium of AM fungi consistently performed better in terms of the parameters evaluated. The study suggests use of mixed consortium of AM fungi over monospecific cultures for the sustainable cultivation and conservation of endangered medicinal plant: Curculigo orchioides.     

Biofertilizers and/or some micronutrients role on wheat plants grown on newly reclaimed soil

Pot experiment was conducted to study the effect of biofertilizers (inoculation with different bacterial isolates), foliar spraying with some micronutrients (Mn, Zn, Fe and Mn+Zn+Fe) and their interaction on growth, physiological parameters and nutrients content of wheat plants grown on reclaimed soil. Pot experiment was conducted in the greenhouse of National Research center, The experimental design was split plot with four replicates. Four biofertilizer treatments (un‐inoculated, Bacillus polymyxa, Azotobacter chroococcum or Azosprillium barasilense) were used and randomly distributed in the main pots. The foliar treatments with micronutrients were randomly distributed in the sub plots. The growth parameters (plant height, leaf area, roots, shoots and whole plant dry weights and number of tillers & leaves per plant); some physiological parameters (soluble sugar %, protein %, polysaccharide %, chl. A+b μg cm^?1 leaf per plant, carotenoids μg g^?1, IAA mg kg^?1 and psll mol DCPIP reduced per mg chl. per h) and nutrient contents (N, P, K, Mg, Mn, Zn and Cu) of wheat plants were significantly increased by inoculating wheat grains with different bacteria as compared with un‐inoculated plants (control). The highest values of all the mentioned parameters were obtained by using Azospirillum brasilense followed by Azotobacter chroococcum and Bacillus polymyxa in decreasing order. Foliar spraying treatments significantly increased the growth parameters, physiological parameters as well as nutrients content of wheat plants as compared with control. Highest values were obtained by using (Mn+Fe+Zn) treatment followed by Zn, Fe and Mn in decreasing order. Micronutrients in wheat plants differed as the foliar treatments were differed, so application of any micronutrient individually significantly increased its content and enhanced the content of other micronutrients in wheat. Interaction between the used biofertilizers and foliar spraying with micronutrients significantly affected all the studied parameters of wheat plants, the highest were obtained by inoculating wheat grains with Azospirillum brasilense and spraying the plants with (Mn+Fe+Zn) treatment, while the lowest values were attained by un‐inoculated grains (control) and spraying the wheat plants with tap water (control). Effective microorganisms in combination with micronutrients could be recommended to farmers to lead higher wheat yield.     

Effectiveness of arbuscular mycorrhizal fungi in phytoremediation of lead- contaminated soil by vetiver grass

A greenhouse experiment was conducted to evaluate the effectiveness of arbuscular mycorrhizal (AM) fungi in phytoremediation of lead (Pb)-contaminated soil by vetiver grass. Experiment was a factorial arranged in a completely randomized design. Factors included four Pb levels (50, 200, 400, and 800 mg kg^?1) as Pb (NO₃)₂, AM fungi at three levels (non mycorrhizal (NM) control, Rhizophagus intraradices, Glomus versiforme). Shoot and root dry weights (SDW and RDW) decreased as Pb levels increased. Mycorrhizal inoculation increased SDW and RDW compared to NM control. With mycorrhizal inoculation and increasing Pb levels, Pb uptake of shoot and root increased compared to those of NM control. Root colonization increased with mycorrhizal inoculation but decreased as Pb levels increased. Phosphorus concentration and uptake in shoot of plants inoculated with AM fungi was significantly higher than NM control at 200 and 800 mg Pb kg^?1. The Fe concentration, Fe and Mn uptake of shoot in plants inoculated with Rhizophagus intraradices in all levels of Pb were significantly higher than NM control. Mycorrhizal inoculation increased Pb extraction, uptake and translocation efficiencies. Lead translocation factor decreased as Pb levels increased; however inoculation with AM fungi increased Pb translocation.     

Functional compatibility in cucumber mycorrhizas in terms of plant growth performance and foliar nutrient composition

Functional compatibility in cucumber mycorrhizas in terms of plant and fungal growth, and foliar nutrient composition from all possible combinations of six cucumber varieties and three species of arbuscular mycorrhizal (AM) fungi was evaluated. Measurements of foliar nutrient composition included N, P, K, Mg, Ca, Na, Fe, Zn, Mn and Cu. Growth of AM fungi was measured in terms of root colonisation, as examined with microscopy and the AM fungus biomarker fatty acid 16:1ω5 from both phospholipids and neutral lipids. Different responses of plant growth and foliar nutrient profiles were observed for the different AM symbioses examined. The AM fungus Claroideoglomus claroideum caused growth depression in association with four out of six cucumber varieties; Rhizophagus irregularis caused growth promotion in one of six cucumber varieties; whereas Funneliformis mosseae had no effect on the growth performance of any of the cucumber varieties examined. All three AM fungi markedly altered host plant shoot nutrient composition, with the strongest contrast observed between cucumber–R. irregularis symbioses and non‐mycorrhizal cucumber plants, independent of cucumber variety. On the other hand, AM fungal growth in roots differed between the three AM fungi, but was unaffected by host genotype. Strong build‐up of storage lipids was observed for R. irregularis, which was more moderate in the two other AM fungi. In conclusion, strong differential responses of cucumber varieties to inoculation with different AM fungi in terms of growth and shoot nutrient composition revealed high functional diversity in AM symbioses in cucumber plants.     

Oxygen cleavage with manganese and iron in ribonucleotide reductase from <Emphasis Type="Italic">Chlamydia trachomatis</Emphasis>

The oxygen cleavage in Chlamydia trachomatis ribonucleotide reductase (RNR) has been studied using B3LYP* hybrid density functional theory. Class Ic C. trachomatis RNR lacks the radical-bearing tyrosine, crucial for activity in conventional class I (subclass a and b) RNR. Instead of the Fe(III)Fe(III)–Tyr(rad) active state, C. trachomatis RNR has a mixed Mn(IV)Fe(III) metal center in subunit II (R2). A mixed MnFe metal center has never been observed as a radical cofactor before. The active state is generated by reductive oxygen cleavage at the metal site. On the basis of calculated barriers for oxygen cleavage in C. trachomatis R2 and R2 from Escherichia coli with a diiron, a mixed manganese–iron, and a dimanganese center, conclusions can be drawn about the effect of changing metals in R2. The oxygen cleavage is found to be governed by two factors: the redox potentials of the metals and the relative stability of the different peroxides. Mn(IV) has higher stability than Fe(IV), and the barrier is therefore lower with a mixed metal center than with a diiron center. With a dimanganese center, an asymmetric peroxide is more stable than the symmetric peroxide, and the barrier therefore becomes too high. Calculated proton-coupled redox potentials are compared to identify three possible R2 active states, the Fe(III)Fe(III)–Tyr(rad) state, the Mn(IV)Fe(III) state, and the Mn(IV)Mn(IV) state. A tentative energy profile of the thermodynamics of the radical transfer from R2 to subunit I is constructed to illustrate how the stability of the active states can be understood from a thermodynamical point of view.     

Indigenous populations of arbuscular mycorrhizal fungi and soil aggregate stability are major determinants of leek (Allium porrum L.) response to inoculation with Glomus intraradices Schenck & Smith or Glomus versiforme (Karsten) Berch

 Knowledge of physical, chemical and biological soil characteristics influencing plant response to inoculation with arbuscular mycorrhizal (AM) fungi would help to distinguish soils where inoculation could be profitable. The relationship between leek (Allium porrum L.) response to mycorrhizal inoculation with Glomus intraradices Schenck & Smith or G. versiforme (Karsten) Berch and soil texture, bulk density, particle density, porosity, pH, organic matter content, available P, K, Ca, Mg, Fe, Zn, Cu, and Mn, soil structure, soil mycorrhizal potential (SM), preceding crop mycorrhizal potential, composition of indigenous mycorrhizal fungal communities, and the abundance of spores of different species, was studied in 81 agricultural soils using Principal Component Analysis and regression analysis. The nature of the indigenous AM fungi population was an important determinant of leek response to inoculation (RTI). In soils with more than 200 μg available P g^–1, SM potential accounted for over 27% of RTI with G. intraradices and G. versiforme, RTI being high in soils with low SM potential. In low P soils, however, a positive relation between the abundance of water stable soil aggregates in the 0.5–2 mm diameter range and RTI was most important. Low soil Zn and high porosity, abundant total mycorrhizal spore as well as scarcity of spores of G. aggregatum and of the group G. etunicatum-rubiforme were also associated to high RTI. The influence of water stable aggregation of soil on RTI was modulated by soil P levels. Abundance of soil aggregates was positively related to RTI at low soil P levels, but negatively related to RTI at high P levels. Different relationships were found between soil variables and spore abundance of different AM fungi species. Some AM species appear to have as yet undefined similarities or complementarities at the biological or ecological levels. Accepted: 23 July 1997