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 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 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.     

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.     

Quantitative structure activity relationships of some pyridine derivatives as corrosion inhibitors of steel in acidic medium

Quantum chemical calculations using the density functional theory (B3LYP/6-31G* DFT) and semi-empirical AM1 methods were performed on ten pyridine derivatives used as corrosion inhibitors for mild steel in acidic medium to determine the relationship between molecular structure and their inhibition efficiencies. Quantum chemical parameters such as total negative charge (TNC) on the molecule, energy of highest occupied molecular orbital (E _HOMO), energy of lowest unoccupied molecular orbital (E _LUMO) and dipole moment (μ) as well as linear solvation energy terms, molecular volume (Vi) and dipolar-polarization (π*) were correlated to corrosion inhibition efficiency of ten pyridine derivatives. A possible correlation between corrosion inhibition efficiencies and structural properties was searched to reduce the number of compounds to be selected for testing from a library of compounds. It was found that theoretical data support the experimental results. The results were used to predict the corrosion inhibition of 24 related pyridine derivatives.     

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.     

Variable mycorrhizal benefits on the reproductive output of Geranium sylvaticum,with special emphasis on the intermediate phenotype

In several gynodioecious species, intermediate sex between female and hermaphrodite has been reported, but few studies have investigated fitness parameters of this intermediate phenotype. Here, we examined the interactions between plant sex and arbuscular mycorrhizal (AM) fungal species affecting the reproductive output of Geranium sylvaticum, a sexually polymorphic plant species with frequent intermediate sexes between females and hermaphrodites, using a common garden experiment. Flowering phenology, AM colonisation levels and several plant vegetative and reproductive parameters, including seed and pollen production, were measured. Differences among sexes were detected in flowering, fruit set, pollen production and floral size. The two AM species used in the present work had different effects on plant fitness parameters. One AM species increased female fitness through increasing seed number and seed mass, while the other species reduced seed mass in all sexes investigated. AM fungi did not affect intermediate and hermaphrodite pollen content in anthers. The three sexes in G. sylvaticum did not differ in their reproductive output in terms of total seed production, but hermaphrodites had potentially larger fathering ability than intermediates due to higher anther number. The ultimate female function – seed production – did not differ among the sexes, but one of the AM fungi used potentially decreased host plant fitness. In addition, in the intermediate sex, mycorrhizal symbiosis functioned similarly in females as in hermaphrodites.     

Host- and virus-induced gene silencing of HOG1-MAPK cascade genes in Rhizophagus irregularis inhibit arbuscule development and reduce resistance of plants to drought stress

Arbuscular mycorrhizal (AM) fungi can form beneficial associations with the most terrestrial vascular plant species. AM fungi not only facilitate plant nutrient acquisition but also enhance plant tolerance to various environmental stresses such as drought stress. However, the molecular mechanisms by which AM fungal mitogen-activated protein kinase (MAPK) cascades mediate the host adaptation to drought stimulus remains to be investigated. Recently, many studies have shown that virus-induced gene silencing (VIGS) and host-induced gene silencing (HIGS) strategies are used for functional studies of AM fungi. Here, we identify the three HOG1 (High Osmolarity Glycerol 1)-MAPK cascade genes RiSte11, RiPbs2 and RiHog1 from Rhizophagus irregularis. The expression levels of the three HOG1-MAPK genes are significantly increased in mycorrhizal roots of the plant Astragalus sinicus under severe drought stress. RiHog1 protein was predominantly localized in the nucleus of yeast in response to 1 M sorbitol treatment, and RiPbs2 interacts with RiSte11 or RiHog1 directly by pull-down assay. Importantly, VIGS or HIGS of RiSte11, RiPbs2 or RiHog1 hampers arbuscule development and decreases relative water content in plants during AM symbiosis. Moreover, silencing of HOG1-MAPK cascade genes led to the decreased expression of drought-resistant genes (RiAQPs, RiTPSs, RiNTH1 and Ri14-3-3) in the AM fungal symbiont in response to drought stress. Taken together, this study demonstrates that VIGS or HIGS of AM fungal HOG1-MAPK cascade inhibits arbuscule development and expression of AM fungal drought-resistant genes under drought stress.     

HLA-DP/DR interaction in early onset pauciarticular juvenile chronic arthritis

We investigated the polymorphic second exon of the HLA-DPB1 and HLA-DRB1 genes, using in vitro DNA amplification by polymerase chain reaction (PCR) and oligonucleotide hybridization in 136 patients with early onset pauciarticular juvenile chronic arthritis (EOPA-JCA) and 199 healthy controls. The analysis of the HLA-DRB1 system revealed that most of the DRB1 alleles are not indifferent with respect to susceptibility to EOPA-JCA. There is a hierarchy of susceptible (DRB1*08, DR5), permissive (DRB1*01), moderately protective (DR2, DRB1*04), and protective (DRB1*07) alleles. In contrast, no hierarchy could be shown for the HLA-DPB1 system. DPB1*0201 was found to be susceptible. The relatively frequent alleles DPB1*0402 and DPB1*0401 seem to be indifferent. The associations with DPB1*0201, DR5, and DRB1*08 are independent of each other: that is to say they, are not brought about by linkage disequilibrium. The susceptible alleles DPB1*0201 and DR5 show evidence for interaction in the pathogenesis of EOPA-JCA. Interaction seems likely between DPB1*0201 and DRB1*08, DR5 and DRB1*08, or between DR6 and DRB1*08. The strongest interaction exists between DPB1*0201 and a common DQ factor associated with both DR5 and DRB1*08. Finally, we observed a hierarchy among the various marker combinations, where the risk of developing EOPA-JCA increases with the number of associated markers present in an individual.This work was supported by SFB217.The data presented here are part of the doctoral thesis of C. Paul.     

HLA-DPB1 alleles in a population from South China

Using the polymerase chain reaction (PCR) and hybridization with oligonucleotide probes, we analyzed the distribution of DPB1 alleles in 99 healthy unrelated individuals from the city of Guangzhou (Canton), South China. Twelve different DPB1 alleles were found in this panel. The most common allele was DPB1*0501 (62.6%). Other major alleles detected included DPB1*02 (DPB1*0201 and DPB1*0202), DPB1*1301, DPB1*0401, and a recently described allele, designated DPB1*2101. The hybridization pattern of DPB1*2101 showed that this allele shared sequences with DPB1*0301 and DPB1*0601 in the A and F hypervariable regions, while the C, D, and E regions were identical to those of DPB1*0202. DPB1*2101 was observed in 11% of the subjects tested. It was found to be in strong linkage dis-equilibrium with DRB1*1202. In family studies, segregation of the haplotype DRB1*1202, DRB3*0301, DQA1*0601, DQB1*0301, DPB1*2101 was observed. The second exon of DPB1*2101 was sequenced from codon 8 to codon 90 and the sequence, inferred from the pattern of hybridization, was confirmed. DPB1*0301, DPB1*0402, DPB1*0101, DPB1*1401, DPB1*1901, and another recently recognized allele, now designated DPB1*2401, were detected with low frequencies. DPB1*2401 had the same hybridization pattern as DPB1*0501 except for a probe that matches codons 85–90. In this region, DPB1*2401 encoded the amino acid sequence GPMTLQ instead of EAVTLQ as in DPB1*0501.     

Evaluation of lipoprotein size-density distributions from sedimentation coefficient distributions obtained at several solvent densities. I. Theory

A method is presented for the treatment of distribution functions obtained by ultra-centrifugal sedimentation velocity experiments on the plasma lipoproteins, so that adequate corrections can he made for the effects of diffusion and concentration dependence of the sedimentation coefficient. The method involves the use of modified equations derived from those presented in 1952 by Gosting for the transform from g* (S) to g(S) distributions. The evaluation of the molecular parameters of lipoprotein density and size, from a set of g(S_i°) distribution functions obtained in solvents of varying density, is also outlined. Preparations of the β-lipoprotein of human plasma are found to follow a bivariate normal distribution that requires evaluation of five parameters, x?₁, σ₁, x?₂, σ₂and p. The first two represent the mean and standard deviation of the lipoprotein density, the third and fourth the same quantities for the size, expressed as ft “logarithmic diameter parameter”, and the final value is a measure of the correlation between these two variables.     

A comparison of wild-type, old and modern tomato cultivars in the interaction with the arbuscular mycorrhizal fungus Glomus mosseae and the tomato pathogen Fusarium oxysporum f. sp. lycopersici

The effect of the arbuscular mycorrhizal symbiosis (AM) varies in plant cultivars. In the present study, we tested whether wild-type, old and modern tomato cultivars differ in the parameters of the AM interaction. Moreover, the bioprotective effect of AM against the soilborne tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol) was tested in the different cultivars. Ten tomato cultivars were inoculated with the arbuscular mycorrhizal fungus (AMF) Glomus mosseae alone or in combination with Fol. At the end of the experiment, AM root colonization, Fusarium infection, and the plant fresh weight was determined. The tomato cultivars differed in their susceptibility to AMF and Fol, but these differences were not cultivar age dependent. In all the cultivars affected by Fol, mycorrhization showed a bioprotective effect. Independent of the cultivar age, tomato cultivars differ in their susceptibility to AMF and Fol and the bioprotective effect of mycorrhization, indicating that the cultivar age does not affect the AM parameters tested in this study.     

3-Iodothyronamine: a novel hormone controlling the balance between glucose and lipid utilisation

3-Iodothyronamine is considered as a derivate of thyroid hormone as a result of enzymatic deiodination and decarboxylation. The physiological role of thyronamine (T1AM) is not known. The aim of this study was to analyze the metabolic response to T1AM in the Djungarian hamster Phodopus sungorus. We measured the influence of T1AM (50 mg/kg) on metabolic rate (VO₂), body temperature (T _b) and respiratory quotient (RQ) in this species and in BL/6 mice. T1AM treated hamsters as well as the mice showed a rapid decrease in VO₂ and T _b, accompanied by a reduction of RQ from normal values of about ∼0.9 to ∼0.70 for several hours. This indicates that carbohydrate utilisation is blocked by the injection of T1AM and that metabolic pathways are rerouted from carbohydrate to lipid utilisation in response to T1AM. This assumption was further supported by the observation that the treatment of T1AM caused ketonuria and a significant loss of body fat. Our results indicate that T1AM has the potential to control the balance between glucose and lipid utilisation in vivo.     

Cereal phosphate transporters associated with the mycorrhizal pathway of phosphate uptake into roots

A very large number of plant species are capable of forming symbiotic associations with arbuscular mycorrhizal (AM) fungi. The roots of these plants are potentially capable of absorbing P from the soil solution both directly through root epidermis and root hairs, and via the AM fungal pathway that delivers P to the root cortex. A large number of phosphate (P) transporters have been identified in plants; tissue expression patterns and kinetic information supports the roles of some of these in the direct root uptake pathways. Recent work has identified additional P transporters in several unrelated species that are strongly induced, sometimes specifically, in AM roots. The primary aim of the work described in this paper was to determine how mycorrhizal colonisation by different species of AM fungi influenced the expression of members of the Pht1 gene families in the cereals Hordeum vulgare (barley), Triticum aestivum (wheat) and Zea mays (maize). RT-PCR and in-situ hybridisation, showed that the transporters HORvu;Pht1;8 (AY187023), TRIae;Pht1;myc (AJ830009) and ZEAma;Pht1;6 (AJ830010), had increased expression in roots colonised by the AM fungi Glomus intraradices,Glomus sp. WFVAM23 and Scutellospora calospora. These findings add to the increasing body of evidence indicating that plants that form AM associations with members of the Glomeromycota have evolved phosphate transporters that are either specifically or preferentially involved in scavenging phosphate from the apoplast between intracellular AM structures and root cortical cells. Operation of mycorrhiza-inducible P transporters in the AM P uptake pathway appears, at least partially, to replace uptake via different P transporters located in root epidermis and root hairs. Electronic Supplementary Material Supplementary material is available for this article at     

Bio-remediation of Pb and Cd polluted soils by switchgrass: A case study in India

Introduction: In the present study bioremediation potential of a high biomass yielding grass, Panicum virgatum (switchgrass), along with plant associated microbes (AM fungi and Azospirillum), was tested against lead and cadmium in pot trials.

Methods: A pot trial was set up in order to evaluate bioremediation efficiency of P. virgatum in association with PAMs (Plant Associated Microbes). Growth parameters and bioremediation potential of endomycorrhizal fungi (AMF) and Azospirillum against different concentrations of Pb and Cd were compared.

Results: AM fungi and Azospirillum increased the root length, branches, surface area, and root and shoot biomass. The soil pH was found towards neutral with AMF and Azospirillum inoculations. The bioconcentration factor (BCF) for Pb (12 mg kg^?1) and Cd (10 mg kg^?1) were found to be 0.25 and 0.23 respectively and translocation index (Ti) was 17.8 and 16.7 respectively (approx 45% higher than control).

Conclusions: The lower values of BCF and Ti, even at highest concentration of Pb and Cd, revealed the capability of switchgrass of accumulating high concentration of Pb and Cd in the roots, while preventing the translocation of Pb and Cd to aerial biomass.