Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA

[Mo(SSCH₃)(S₂C₂(CH₃)₂)₂] ^x complexes with charges x between −3 and +3 were investigated by density functional theory computations as minimal nitrate reductase active-site models. The strongly reduced species (x = −2, −3) exist preferentially as pentacoordinate sulfo complexes separated from a thiolate anion. The oxidized extremes (x > 0) clearly prefer hexacoordinate complexes with an η²-MeSS ligand. Among the neutral and especially for the singly negatively charged species structures with η²-MeSS and η¹-MeSS ligands are energetically close to the sulfo methyl sulfide complex without SS bonding. For x = −1 the three isomers lie in a 1.5 kcal mol⁻¹ energy range. Putative mechanistic pathways for nitrate reduction from the literature were investigated computationally: (1) reduction at a pentacoordinate sulfo complex, (2) reduction at the ligand, and (3) reduction at the molybdenum center with an R–S–S ligand. All three pathways could be traced at least for some overall charges but no definite conclusion can be drawn about the mechanism. Complexes with larger dithiolato ligands were also computed in order to model the tricyclic metallopterin framework more accurately: the first heterocyclus (5,6-dihydro-2H-pyran) stabilizes the nitrate complex and the molybdenum oxo product complex by approximately 10 kcal mol⁻¹ and also reduces the activation barrier (by approximately 5 kcal mol⁻¹). The effect of the second (1,2,3,4-tetrahydropyrazin) and third heterocyclus (2-amino-3H-pyrimidin-4-one) on the relative energies is relatively small. For bigger models derived from an experimental protein structure, nitrate reduction at a persulfo molybdenum(IV) complex fragment (mechanism 3) is clearly favored over the oxidation of a molybdenum-bound sulfur atom (mechanism 2). Mechanism 1 could not be investigated for the big models but seems the least favorable on the basis of the results from smaller models.     

Theoretical study of N<Subscript>4</Subscript>X (X = O,S, Se) systems

A series of N₄X (X = O, S, Se) compounds have been examined with ab initio and density functional theory (DFT) methods. To our knowledge, these compounds, except for the C_2v ring and the C_3v towerlike isomers of N₄O, are first reported here. The ring structures are the most energetically favored for N₄X (X = O and S) systems. For N₄Se, the cagelike structure is the most energetically favored. Several decomposition and isomerization pathways for the N₄X species have been investigated. The dissociation of C_2v ring N₄O and N₄S structures via ring breaking and the barrier height are only 1.1 and −0.2 kcal mol⁻¹ at the CCSD(T)/6-311+G*//MP2/6-311+G* level of theory. The dissociation of the cagelike N₄X species is at a cost of 12.1–16.2 kcal mol⁻¹. As for the towerlike and triangle bipyramidal isomers, their decomposition or isomerization barrier heights are all lower than 10.0 kcal mol⁻¹. Although the C_S cagelike N₄S isomer has a moderate isomerization barrier (18.3–29.1 kcal mol⁻¹), the low dissociation barrier (−1.0 kcal mol⁻¹) indicates that it will disappear when going to the higher CCSD(T) level. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effect of light and nitrates on nitrate reductase activity and stability in seedling leaves of selected barley genotypes

Parental genotypes (cv. Aramir and line R567) and the selected doubled haploid (DH) lines C23, C47/1, C41, C55 did not differ in NR activity when they grew on a nutrient solution containing 10 mM KNO₃ and were illuminated with light at 124 μmol·m⁻²·s⁻¹ intensity. A decrease of nitrate content in the nutrient medium to 0.5 mM at 44 μmol·m⁻²·s⁻¹ light intensity caused a significant reduction of NR activity in the parental genotypes as well as in the lines C41 and C55. An increase in light intensity to 124 μmol·m⁻²·s⁻¹ raised NR activity in the leaf extracts of these genotypes. However, independently of light intensity, a high level of this enzyme activity was maintained in the line C23 growing on the nutrient medium with 10 mM and 0.5 mM KNO₃. The NR activity in that line dropped only when nitrate content in the medium decreased to 0.1 mM. NR in the leaves of the line C23, as compared to C41, was characterized by a higher thermal stability in all experimental combinations. An increase in light intensity had no significant influence on NR thermal stability in the leaves of the line C41, but induced a significant increase of this enzyme stability in the line C23. The lines C23 and C41 growing on the nutrient medium with 0.5 mM KNO₃ differed appreciably by nitrate concentration in leaves. A higher accumulation of nitrates was detected in the leaves of the line C41.     

Effect of phytohormones and tungsten on light-induced and nitrate-induced nitrate reductase activity of mustard cotyledons

Mustard (Brassica juncea Coss cv. T-59 ‘Varuna’) seedlings pretreated with gibberellic acid (GA) and kinetin (KiN) were grown in light. In vivo nitrate reductase (NR) activity was estimated and effect of tungsten on light-induced and NO ₃ ^su− -induced NR activity was investigated. Different concentrations of GA did not show any effect on induction of light-induced NR; addition of nitrate promoted in vivo NR activity but no concentration effect of GA was evident. Light-induced NR was promoted by KiN and like in GA treatment, addition of nitrate increased NR activity. Addition of Na-tungstate inhibited NO ₃ ⁻ induced NR while light-induced NR was not much affected in both GA and KiN treated seedlings. The two forms of NRs were further characterized by studying the decay kinetics using Na-tungstate. In light-induced NR, tungstate did not affect NR activity up to 11 h, while at later periods, a slight decay was observed. On the other hand, NO ₃ ⁻ -induced NR activity increased up to 4 h and subsequently a rapid fall was observed. It was therefore apparent that light-induced NR had a very low turnover rate as compared to NO ₃ ⁻ -induced NR. These results further support the earlier conclusion that in mustard seedlings two distinct types of NR enzyme exist and that nitrate requirement for NR induction is not absolute.     

Theoretical study of hydrogenation of the doubly aromatic B 7 − cluster

We have studied the influence of hydrogenation on the relative stability of the low-lying isomers of the anionic B₇⁻ cluster, computationally. It is known that the pure-boron B₇⁻ cluster has a doubly (σ- and π-) aromatic C_6v (³A₁) quasi-planar wheel-type triplet global minimum (structure 1), a low-lying σ-aromatic and π-antiaromatic quasi-planar singlet C_2v (¹A₁) isomer 2 (0.7 kcal mol⁻¹ above the global minimum), and a planar doubly (σ- and π-) antiaromatic C_2v (¹A₁) isomer 3 (7.8 kcal mol⁻¹ above the global minimum). However, upon hydrogenation, an inversion in the stability of the species occurs. The planar B₇H₂⁻ (C_2v, ¹A₁) isomer 4, originated from the addition of two hydrogen atoms to the doubly antiaromatic B₇⁻ isomer 3, becomes the global minimum structure. The second most stable B₇H₂⁻ isomer 5, originated from the quasi-planar triplet wheel isomer 1 of B₇⁻, was found to be 27 kcal mol⁻¹ higher in energy. The inversion in stability occurs due to the loss of the doubly aromatic character in the wheel-type global minimum isomer (C_6v, ³A₁) of B₇⁻ upon H₂−addition. In contrast, the planar isomer of B₇⁻ (C_2v, ¹A₁) gains aromatic character upon addition of two hydrogen atoms, which makes it more stable. Figure The B₇H₂-global minimum structure and its σ-aromatic and π-antiaromatic MOs Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday.     

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol⁻¹. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol⁻¹. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol⁻¹. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries. Figure Calculated structure of the complex ion [Ta₆Cl₁₂]²⁺ (footnote): Reference value in parenthesis Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Is photosynthetic acclimation to free-air CO<Subscript>2</Subscript> enrichment (FACE) related to a strong competition for the assimilatory power between carbon assimilation and nitrogen assimilation in rice leaf?

Net photosynthetic rate (P _N) of leaves grown under free-air CO₂ enriched condition (FACE, about 200 μmol mol⁻¹ above ambient air) was significantly lower than P _N of leaves grown at ambient CO₂ concentration (AC) when measured at CO₂ concentration of 580 μmol mol⁻¹. This difference was found in rice plants grown at normal nitrogen supply (25 g m⁻²; NN-plants) but not in plants grown at low nitrogen supply (15 g m⁻²; LN-plants). Namely, photosynthetic acclimation to FACE was observed in NN-plants but not in LN-plants. Different from the above results measured in a period of continuous sunny days, such photosynthetic acclimation occurred in NN-plants, however, it was also observed in LN-plants when P _N was measured before noon of the first sunny day after rain. Hence strong competition for the assimilatory power between nitrogen (N) and carbon (C) assimilations induced by an excessive N supply may lead to the photosynthetic acclimation to FACE in NN-plants. The hypothesis is supported by the following facts: FACE induced significant decrease in both apparent photosynthetic quantum yield (Φ_c) and ribulose-1,5-bisphosphate (RuBP) content in NN-plants but not in LN-plants.     

Nitrate Reductase Activity in an Eutrophic Reservoir duringthe Stratification Cycle

Nitrate reductase activity was measured during the stratification cycle of the eutrophic reservoir La Concepción. Nitrate was consumed in the epilimnion mainly through assimilatory reduction, and in the hypolimnion through dissimilatory reduction triggered by anoxic conditions. Nitrate reductase activity (NR) scaled to particulate nitrogen (PN) was positively correlated with the external nitrate concentration and the NO₃^–/NH₄⁺ ratio. Using NR as a tool for the assessment of the N cycle dynamics, it can be suggested that at the beginning of the stratification cycle, the phytoplanktonic community was mainly using NO₃^– as N source; and since N was not likely the limiting nutrient at that time of the year, NR was close to its maximum possible.     

Modeling nitrogen cycling in a coastal fresh water sediment

Increased nitrogen (N) loading to coastal marine and freshwater systems is occurring worldwide as a result of human activities. Diagenetic processes in sediments can change the N availability in these systems, by supporting removal through denitrification and burial of organic N (N_org) or by enhancing N recycling. In this study, we use a reactive transport model (RTM) to examine N transformations in a coastal fresh water sediment and quantify N removal rates. We also assess the response of the sediment N cycle to environmental changes that may result from increased salinity which is planned to occur at the site as a result of an estuarine restoration project. Field results show that much of the N_org deposited on the sediment is currently remineralized to ammonium. A rapid removal of nitrate is observed in the sediment pore water, with the resulting nitrate reduction rate estimated to be 130 μmol N cm⁻² yr⁻¹. A model sensitivity study was conducted altering the distribution of nitrate reduction between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification. These results show a 40% decline in sediment N removal as NO ₃ ⁻ reduction shifts from denitrification to DNRA. This decreased N removal leads to a shift in sediment-water exchange flux of dissolved inorganic nitrogen (DIN) from near zero with denitrification to 133 μmol N cm⁻² yr⁻¹ if DNRA is the dominant pathway. The response to salinization includes a short-term release of adsorbed ammonium. Additional changes expected to result from the estuarine restoration include: lower NO ₃ ⁻ concentrations and greater SO ₄ ²⁻ concentrations in the bottom water, decreased nitrification rates, and increased sediment mixing. The effect of these changes on net DIN flux and N removal vary based on the distribution of DNRA versus denitrification, illustrating the need for a better understanding of factors controlling this competition.     

Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches

The 3D structure of the amidase from Rhodococcus erythropolis (EC 3.5.1.4) built by homology-based modeling is presented. Propionamide and acetamide are docked to the amidase. The reaction models were used to characterize the explicit enzymatic reaction. The calculated free energy barrier at B3LYP/6-31G* level of Model A (Ser194 + propionamide) is 19.72 kcal mol⁻¹ in gas (6.47 kcal mol⁻¹ in solution), and of Model B (Ser194 + Gly193 + propionamide) is 18.71 kcal mol⁻¹ in gas (4.57 kcal mol⁻¹ in solution). The docking results reveal that propionamide binds more strongly than acetamide due to the ethyl moiety of propionamide, which makes the carboxyl oxygen center of the substrate slightly more negative, making formation of the positively charged tetrahedral intermediate slightly easier. The quantum mechanics results demonstrate that Ser194 is essential for the acyl-intermediate, and Gly193 plays a secondary role in stabilizing acyl-intermediate formation as the NH groups of Ser194 and Gly193 form hydrogen bonds with the carbonyl oxygen of propionamide. The new structural and mechanistic insights gained from this computational study should be useful in elucidating the detailed structures and mechanisms of amidase and other homologous members of the amidase signature family.     

The Fate of 15N-Nitrate in Healthy and Declining Phragmites australis Stands

Abstract The dissimilatory nitrate-reducing processes, denitrification, and dissimilatory nitrate-reduction to ammonium were studied in freshwater lake sediments within healthy and degrading Phragmites australis (reed) stands. The samples from the healthy vegetation site contained roots and rhizomes. Cores were supplied with 1.9–5.2 μg ¹⁵N-NO₃ ⁻ g⁻¹ dry sediment in the laboratory and subsequently incubated for 8 h at 20°C, in the dark. The ¹⁵N compounds were determined before (natural percentage of ¹⁵N) and after 1 and 8 h of incubation. The uptake of ¹⁵N by the roots and rhizomes in the healthy vegetation was 61%. Nitrogen losses, interpreted as denitrification, accounted for 25 and 84% of the added ¹⁵N-NO₃ ⁻ in sediment from the healthy and degrading vegetation sites, respectively. The percentages of nitrate reduced to ammonium were 4 and 9% in sediment from the healthy vegetation and degrading vegetation sites, respectively. The percentage of ¹⁵N–total N in the sediment of the healthy vegetation site was 10%, whereas for the degrading vegetation site this percentage was 7%. The percentage of nitrate reduced to ammonium could be potentially underestimated by the percentage of ¹⁵N measured in the sediment. In this case, in healthy and degenerating P. australis stands, the percentage of produced ammonium accounted for 14–16%. The nitrate reduction rates were calculated based on an incubation period of one hour. The denitrification rate in sediment from the degrading vegetation site was higher than from the healthy vegetation site. The rate of dissimilatory nitrate reduction to ammonium was almost tenfold higher in sediment from the degrading vegetation site compared to sediment from the healthy vegetation site. The significantly lower percentages of dissimilatory nitrate reduction to ammonium and denitrification in the healthy stand compared to the degrading stand was probably due to the presence of roots and rhizomes. In the sediments of healthy and degrading P. australis stands, denitrification was the main nitrate-reducing process. Received: 24 July 1996; Accepted: 5 December 1996     

Physiological alterations and regulation of heterocyst and nitrogenase formation in Het(-) Fix(-) mutant strain of Anabaena variabilis

Physiological alterations and regulation of heterocyst and nitrogenase formation have been studied in Het⁻ Fix⁻ mutant strain of diazotrophic cyanobacterium Anabaena variabilis. Het⁻ Fix⁻ mutant strain of A. variabilis has been isolated by N-methyl-N′-nitro-N″-nitrosoguanidine (NTG) mutagenesis and was screened with the penicillin enrichment (500 μg ml⁻¹). Growth, heterocyst differentiation, nitrogenase and glutamine synthetase (biosynthetic and transferase), ¹⁴CO₂-fixation, nitrate reductase (NR), nitrite reductase (NiR), glucose-6-phosphate dehydrogenase (G6PDH), and isocitrate dehydrogenase (IDH) activities, and NO₃ ⁻, NO₂ ⁻, and NH₄ ⁺ uptake and whole cell protein profile in different metabolic conditions were studied in the Het⁻ Fix⁻ mutant strain taking wild-type A. variabilis as reference. Het⁻ Fix⁻ mutant strain was incapable of assimilating elemental nitrogen (N₂) due to its inability to form heterocysts and nitrogenase and this was the reason for its inability to grow in BG-11₀ medium (free from combined nitrogen). In contrast, wild-type strain grew reasonably well in the absence of combined nitrogen sources and also showed heterocyst differentiation (8.5%) and nitrogenase activity (10.8 ηmol C₂H₄ formed μg⁻¹ Chl a h⁻¹) in N₂-medium. Wild-type strain also exhibited higher NR, NiR, and GS activities compared to its Het⁻ Fix⁻ mutant strain, which may presumably be due to acquisition of high uptake of NO₃ ⁻, NO₂ ⁻, and NH₂ ⁺. Wild-type strain in contrast to its Het⁻ Fix⁻ mutant strain also exhibited high level of G6PDH, IDH, and ¹⁴CO₂ fixation activities. Low levels of G6PDH and IDH activities in Het⁻ Fix⁻ mutant strain further confirmed the lack of heterocyst differentiation and nitrogenase activity in the Het⁻ Fix⁻ mutant strain. NR, NiR, and GS activities in both the strains were energy-dependent and the energy required is mainly derived from photophosphorylation. Furthermore, it was found that de novo protein synthesis is necessarily required for the activities of NR, NiR, and GS in both wild-type and its Het⁻ Fix⁻ mutant strain. Received: 21 December 2001 / Accepted: 28 January 2002     

Denitrification,dissimilatory nitrate reduction to ammonium,and nitrogen fixation along a nitrate concentration gradient in a created freshwater wetland

Wetlands are often highly effective nitrogen (N) sinks. In the Lake Waco Wetland (LWW), near Waco, Texas, USA, nitrate (NO₃⁻) concentrations are reduced by more than 90% in the first 500 m downstream of the inflow, creating a distinct gradient in NO₃⁻ concentration along the flow path of water. The relative importance of sediment denitrification (DNF), dissimilatory NO₃⁻ reduction to ammonium (DNRA), and N₂ fixation were examined along the NO₃⁻ concentration gradient in the LWW. “Potential DNF” (hereafter potDNF) was observed in all months and ranged from 54 to 278 μmol N m⁻² h⁻¹. “Potential DNRA” (hereafter potDNRA) was observed only in summer months and ranged from 1.3 to 33 μmol N m⁻² h⁻¹. Net N₂ flux ranged from 184 (net denitrification) to −270 (net N₂ fixation) μmol N m⁻² h⁻¹. Nitrogen fixation was variable, ranging from 0 to 426 μmol N m⁻² h⁻¹, but high rates ranked among the highest reported for aquatic sediments. On average, summer potDNRA comprised only 5% (±2% SE) of total NO₃⁻ loss through dissimilatory pathways, but was as high as 36% at one site where potDNF was consistently low. Potential DNRA was higher in sediments with higher sediment oxygen demand (r ² = 0.84), and was related to NO₃⁻ concentration in overlying water in one summer (r ² = 0.81). Sediments were a NO₃⁻ sink and accounted for 50% of wetland NO₃⁻ removal (r ² = 0.90). Sediments were an NH₄⁺ source, but the wetland was often a net NH₄⁺ sink. Although DNRA rates in freshwater wetlands may rival those observed in estuarine systems, the importance of DNRA in freshwater sediments appears to be minor relative to DNF. Furthermore, sediment N₂ fixation can be extremely high when NO₃⁻ in overlying water is consistently low. The data suggest that newly fixed N can support sustained N transformation processes such as DNF and DNRA when surface water inorganic N supply rates are low.     

Short-term inhibition of legume N2 fixation by nitrate

The hypothesis of NO ₂ ⁻ toxicity as the causative factor of NO ₃ ⁻ inhibition of nitrogenase (N₂ase; EC 1.18.6.1) activity has been evaluated using a short-term exposure (3 d) of several legumes. Treatment of plants with 10 mM NO ₃ ⁻ induced nitrate reductase (NR) from bacteroids (EC 1.7.99.4) and nodule cytosol (EC 1.6.6.1) in most species. Regardless of the levels of both enzymes, significant accumulation of NO ₂ ⁻ did not occur in nodules. Dissection of nodules into cortical and infected regions, and subsequent NO ₂ ⁻ assays in conditions that suppressed enzyme activities, indicated that, in the short-term, bacteroid NR does not generate NO ₂ ⁻ in vivo. This is probably because NO ₃ ⁻ access is restricted to the nodule cortex. Accumulation of NO ₂ ⁻ at levels that are damaging for N₂ase and leghaemoglobin were only observed when a delay occurred between dissection and assaying of nodules. It is concluded that NO ₂ ⁻ is not responsible for the initial NO ₃ ⁻ -induced decline of N₂ase activity, and that toxic amounts of NO ₂ ⁻ only build up in nodules following longer exposures to NO ₃ ⁻ , when this anion is actively reduced by bacteroid and cytosol enzymes.     

Isolation and characterization of nitrite-reductase-deficient mutants of Chlorella sorokiniana (strain 211-8k)

 A method is presented to isolate mutants of Chlorella sorokiniana with defects in NO₃ ⁻ metabolism. Three nitrite-reductase (NIR; E.C.1.7.7.1)-deficient mutants were obtained from 500 pinpoint-colony-forming clones. The final screening was performed using NO₃ ⁻, NO₂ ⁻ or NH⁺ ₄ as N-source. The mutants isolated absorb NO₃ ⁻ with rates close to those measured for the wild type and they excrete NO₂ ⁻ into the medium. The ratio between NO₃ ⁻ uptake and NO₂ ⁻ excretion was 1:1. The sensitivity of NO₃ ⁻ uptake to NH⁺ ₄ was reduced in the mutant strains as it was in the N-starved wild type of Chlorella. Nitrate reductase (NR; EC 1.6.6.1) expression and NR activity were slightly reduced compared to the wild type due to feedback regulation in the mutant strains. No NIR protein was found in the three mutants. However, NIR activity was obtained (50% of the wild-type) for one mutant strain. The NIR-deficient mutants and the already available NR-deficient mutants will be promising tools for investigations of the nitrate assimilation pathway on the molecular level and for studies searching for signaling of C and N metabolism by inorganic N-compounds. Received: 8 October 1999 / Accepted: 25 January 2000     

The effect of ammonium on assimilatory nitrate reduction in the haloarchaeon Haloferax mediterranei

Physiology, regulation and biochemical aspects of the nitrogen assimilation are well known in Prokarya or Eukarya but they are poorly described in Archaea domain. The haloarchaeon Haloferax mediterranei can use different nitrogen inorganic sources (NO₃⁻, NO₂⁻ or NH₄⁺) for growth. Different approaches were considered to study the effect of NH₄⁺ on nitrogen assimilation in Hfx. mediterranei cells grown in KNO₃ medium. The NH₄⁺ addition to KNO₃ medium caused a decrease of assimilatory nitrate (Nas) and nitrite reductases (NiR) activities. Similar effects were observed when nitrate-growing cells were transferred to NH₄⁺ media. Both activities increased when NH₄⁺ was removed from culture, showing that the negative effect of NH₄⁺ on this pathway is reversible. These results suggest that ammonium causes the inhibition of the assimilatory nitrate pathway, while nitrate exerts a positive effect. This pattern has been confirmed by RT-PCR. In the presence of both NO₃⁻ and NH₄⁺, NH₄⁺ was preferentially consumed, but NO₃⁻ uptake was not completely inhibited by NH₄⁺ at prolonged time scale. The addition of MSX to NH₄⁺ or NO₃⁻ cultures results in an increase of Nas and NiR activities, suggesting that NH₄⁺ assimilation, rather than NH₄⁺ per se, has a negative effect on assimilatory nitrate reduction in Hfx. mediterranei. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Validation of density functional modeling protocols on experimental bis(μ-oxo)/μ-η<Superscript>2</Superscript>:η<Superscript>2</Superscript>-peroxo dicopper equilibria

The bis(μ-oxo)/μ-η²:η²-peroxo equilibria for seven supported Cu₂O₂ cores were studied with different hybrid and nonhybrid density functional theory models, namely, BLYP, mPWPW, TPSS, TPSSh, B3LYP, mPW1PW, and MPW1K. Supporting ligands 3,3′-iminobis(N,N-dimethylpropylamine), N,N,N′,N′,N″-pentamethyldipropylenetriamine, N-[2-(pyridin-2-yl)ethyl]-N,N,N′-trimethylpropane-1,3-diamine, bis[2-(2-pyridin-2-yl)ethyl]methylamine, bis[2-(4-methoxy-2-pyridin-2-yl)ethyl]methylamine, bis[2-(4-N,N-dimethylamino-2-pyridin-2-yl)ethyl]methylamine, and 1,4,7-triisopropyl-1,4,7-triazacyclononane were chosen on the basis of the availability of experimental data for comparison. Density functionals were examined with respect to their ability accurately to reproduce experimental properties, including, in particular, geometries and relative energies for the bis(μ-oxo) and side-on peroxo forms. While geometries from both hybrid and nonhybrid functionals were in good agreement with experiment, the incorporation of Hartree–Fock (HF) exchange in hybrid density functionals was found to have a large, degrading effect on predicted relative isomer energies. Specifically, hybrid functionals predicted the μ-η²:η²-peroxo isomer to be too stable by roughly 5–10 kcal mol⁻¹ for each 10% of HF exchange incorporated into the model. Continuum solvation calculations predict electrostatic effects to favor bis(μ-oxo) isomers by 1–4 kcal mol⁻¹ depending on ligand size, with larger ligands having smaller differential solvation effects. Analysis of computed molecular partition functions suggests that nonzero measured entropies of isomerization are likely to be primarily associated with interactions between molecular solutes and their first solvation shell. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Nitrate reductase activity of two leafy vegetables as affected by nickel and different nitrogen forms

The author studied the effect of different nickel concentrations (0, 0.4, 40 and 80 μM Ni) on the nitrate reductase (NR) activity of New Zealand spinach (Tetragonia expansa Murr.) and lettuce (Lactuca sativa L. cv. Justyna) plants supplied with different nitrogen forms (NO₃ ⁻–N, NH₄ ⁺–N, NH₄NO₃). A low concentration of Ni (0.4 μM) did not cause statistically significant changes of the nitrate reductase activity in lettuce plants supplied with nitrate nitrogen (NO₃ ⁻–N) or mixed (NH₄NO₃) nitrogen form, but in New Zealand spinach leaves the enzyme activity decreased and increased, respectively. The introduction of 0.4 μM Ni in the medium containing ammonium ions as a sole source of nitrogen resulted in significantly increased NR activity in lettuce roots, and did not cause statistically significant changes of the enzyme activity in New Zealand spinach plants. At a high nickel level (Ni 40 or 80 μM), a significant decrease in the NR activity was observed in New Zealand spinach plants treated with nitrate or mixed nitrogen form, but it was much more marked in leaves than in roots. An exception was lack of significant changes of the enzyme activity in spinach leaves when plants were treated with 40 μM Ni and supplied with mixed nitrogen form, which resulted in the stronger reduction of the enzyme activity in roots than in leaves. The statistically significant drop in the NR activity was recorded in the aboveground parts of nickel-stressed lettuce plants supplied with NO₃ ⁻–N or NH₄NO₃. At the same time, there were no statistically significant changes recorded in lettuce roots, except for the drop of the enzyme activity in the roots of NO₃ ⁻-fed plants grown in the nutrient solution containing 80 μM Ni. An addition of high nickel doses to the nutrient solution contained ammonium nitrogen (NH₄ ⁺–N) did not affect the NR activity in New Zealand spinach plants and caused a high increase of this enzyme in lettuce organs, especially in roots. It should be stressed that, independently of nickel dose in New Zealand spinach plants supplied with ammonium form, NR activity in roots was dramatically higher than that in leaves. Moreover, in New Zealand spinach plants treated with NH₄ ⁺–N the enzyme activity in roots was even higher than in those supplied with NO₃ ⁻–N.     

Determination of shelf life of <Emphasis Type="Italic">Spirulina platensis</Emphasis> (MI<Subscript>2</Subscript>) grown in the Philippines

Gamma linolenic acid (GLA) degradation in Spirulina followed first-order reaction kinetics. At an accelerated temperature range of 45 to 55°C, the degradation rate constants (k _r) of GLA obtained were 4.0 × 10⁻² to 8.8 × 10⁻² day⁻¹. The energy of activation (E _a) was 16.53 kcal mol⁻¹, and the Q₁₀ was 2.22. Based on 20% GLA degradation, the shelf life of sun-dried Spirulina at 30°C is 263 days or 8.6 months using the Arrhenius plot, and 258 days or 8.5 months using the Q ₁₀ approach. Presented at the 6th Meeting of the Asia Pacific Society of Applied Phycology, Manila, Philippines.     

Seasonal nutrient fluxes variability of northern salt marshes: examples from the lower St. Lawrence Estuary

This study presents the tidal exchange of ammonium, nitrite + nitrate, phosphate and silicate between two salt marshes and adjacent estuarine waters. Marsh nutrient fluxes were evaluated for Pointe-au-Père and Pointe-aux-épinettes salt marshes, both located along the south shore of the lower St. Lawrence Estuary in Rimouski area (QC, Canada). Using nutrients field data, high precision bathymetric records and a hydrodynamic numerical model (MIKE21-NHD) forced with predicted tides, nutrients fluxes were estimated through salt marsh outlet cross-sections at four different periods of the year 2004 (March, May, July and November). Calculated marsh nutrient fluxes are discussed in relation with stream inputs, biotic and abiotic marsh processes and the incidence of sea ice cover. In both marshes, the results show the occurrence of year-round and seaward NH₄ ⁺ fluxes and landward NO₂ ⁻ + NO₃ ⁻ fluxes (ranging from 9.06 to 30.48 mg N day⁻¹ m⁻² and from −32.07 to −9.59 mg N day⁻¹ m⁻², respectively) as well as variable PO₄ ³⁻ and Si(OH)₄ fluxes (ranging from −3.73 to 6.34 mg P day⁻¹ m⁻² and from −29.19 to 21.91 mg Si day⁻¹ m⁻², respectively). These results suggest that NO₂ ⁻ + NO₃ ⁻ input to marshes can be a significant source of NH₄ ⁺ through dissimilatory nitrate reduction to ammonium (DNRA). This NH₄ ⁺, accumulating in marsh sediment rather than being removed through coupled nitrification–denitrification or biological assimilation, is exported toward estuarine waters. From average P and Si tidal fluxes analysis, both salt marshes act as a sink during high productivity period (May and July) and as a source, supplying estuarine water during low productivity period (November and March).