DFT modeling on the suitable crown ether architecture for complexation with Cs<Superscript>+</Superscript> and Sr<Superscript>2+</Superscript> metal ions

Crown ether architectures were explored for the inclusion of Cs⁺ and Sr²⁺ ions within nano-cavity of macrocyclic crown ethers using density functional theory (DFT) modeling. The modeling was undertaken to gain insight into the mechanism of the complexation of Cs⁺ and Sr²⁺ ion with this ligand experimentally. The selectivity of Cs⁺ and Sr²⁺ ions for a particular size of crown ether has been explained based on the fitting and binding interaction of the guest ions in the narrow cavity of crown ethers. Although, Di-Benzo-18-Crown-6 (DB18C6) and Di-Benzo-21-Crown-7 (DB21C7) provide suitable host architecture for Sr²⁺ and Cs⁺ ions respectively as the ion size match with the cavity of the host, but consideration of binding interaction along with the cavity matching both DB18C6 and DB21C7 prefers Sr²⁺ ion. The calculated values of binding enthalpy of Cs metal ion with the crown ethers were found to be in good agreement with the experimental results. The gas phase binding enthalpy for Sr²⁺ ion with crown ether was higher than Cs metal ion. The ion exchange reaction between Sr and Cs always favors the selection of Sr metal ion both in the gas and in micro-solvated systems. The gas phase selectivity remains unchanged in micro-solvated phase. We have demonstrated the effect of micro-solvation on the binding interaction between the metal ions (Cs⁺ and Sr²⁺) and the macrocyclic crown ethers by considering micro-solvated metal ions up to eight water molecules directly attached to the metal ion and also by considering two water molecules attached to metal-ion-crown ether complexes. A metal ion exchange reaction involving the replacement of strontium ion in metal ion-crown ether complexes with cesium ion contained within a metal ion-water cluster serves as the basis for modeling binding preferences in solution. The calculated O-H stretching frequency of H₂O molecule in micro-solvated metal ion-crown complexes is more red-shifted in comparison to hydrated metal ions. The calculated IR spectra can be compared with an experimental spectrum to determine the presence of micro-solvated metal ion–crown ether complexes in extractant phase.     

A UB3LYP and UMP2 theoretical investigation on unusual cation–π interaction between the triplet state HB=BH ( {}^3\Sigma_g^{-} ) and H+, Li+, Na+, Be2+ or Mg2+

The nature of the unusual cation–π interactions between cations (H⁺, Li⁺, Na⁺, Be²⁺ and Mg²⁺) and the electron-deficient B=B bond of the triplet state HB=BH ( $ {}^3\Sigma_g^{-} $ ) was investigated using UMP2(full) and UB3LYP methods at 6–311++G(2df,2p) and aug-cc-pVTZ levels, accompanied by a comparison with 1:1 and 2:1 σ-binding complexes between BH and the cations. The binding energies follow the order HB=BH...H⁺ > HB=BH...Be²⁺ > HB=BH...Mg²⁺ ? HB=BH...Li⁺ > HB=BH...Na⁺ and HB=BH (¹Δ_g)...M⁺/M²⁺ > H₂C=CH₂...M⁺/M²⁺ > HC≡CH...M⁺/M²⁺ > HB=BH ( $ {}^3\Sigma_g^{-} $ )...M⁺/M²⁺. Furthermore, except for HB...H⁺, the σ-binding interaction energy of the 1:1 complex HB...M⁺/M²⁺ is stronger than the cation–π interaction energy of the C₂H₂...M⁺/M²⁺, C₂H₄...M⁺/M²⁺, B₂H₂ (¹Δ_g)...M⁺/M²⁺ or B₂H₂ ( $ {}^3\Sigma_g^{-} $ )...M⁺/M²⁺ complex, and, for the 2:1 σ-binding complexes, except for HBBe²⁺...BH, they are less stable than the cation–π complexes of B₂H₂ (¹Δ_g) or B₂H₂ ( $ {}^3\Sigma_g^{-} $ ). The atoms in molecules (AIM) theory was also applied to verify covalent interactions in the H⁺ complexes and confirm that HB=BH ( $ {}^3\Sigma_g^{-} $ ) can be a weaker π-electron donor than HB=BH (¹Δ_g), H₂C=CH₂ or HC≡CH in the cation–π interaction. Analyses of natural bond orbital (NBO) and electron density shifts revealed that the origin of the cation–π interaction is mainly that many of the lost densities from the π-orbital of B=B and CC multiple bonds are shifted toward the cations.

Mechanisms of Na+ uptake,ammonia excretion,and their potential linkage in native Rio Negro tetras (Paracheirodon axelrodi,Hemigrammus rhodostomus,and Moenkhausia diktyota)

Mechanisms of Na⁺ uptake, ammonia excretion, and their potential linkage were investigated in three characids (cardinal, hemigrammus, moenkhausia tetras), using radiotracer flux techniques to study the unidirectional influx (J _in), efflux (J _out), and net flux rates (J _net) of Na⁺ and Cl^?, and the net excretion rate of ammonia (J _Amm). The fish were collected directly from the Rio Negro, and studied in their native “blackwater” which is acidic (pH 4.5), ion-poor (Na⁺, Cl^? ~20 µM), and rich in dissolved organic matter (DOM 11.5 mg C l^?1). J _in ^Na , J _in ^Cl , and J _Amm were higher than in previous reports on tetras obtained from the North America aquarium trade and/or studied in low DOM water. In all three species, J _in ^Na was unaffected by amiloride (10^?4 M, NHE and Na⁺ channel blocker), but both J _in ^Na and J _in ^Cl were virtually eliminated (85–99 % blockade) by AgNO₃ (10^?7 M). A time course study on cardinal tetras demonstrated that J _in ^Na blockade by AgNO₃ was very rapid (<5 min), suggesting inhibition of branchial carbonic anhydrase (CA), and exposure to the CA-blocker acetazolamide (10^?4 M) caused a 50 % reduction in J _in ^Na _.. Additionally, J _in ^Na was unaffected by phenamil (10^?5 M, Na⁺ channel blocker), bumetanide (10^?4 M, NKCC blocker), hydrochlorothiazide (5 × 10^?3 M, NCC blocker), and exposure to an acute 3 unit increase in water pH. None of these treatments, including partial or complete elimination of J _in ^Na (by acetazolamide and AgNO₃ respectively), had any inhibitory effect on J _Amm. Therefore, Na⁺ uptake in Rio Negro tetras depends on an internal supply of H⁺ from CA, but does not fit any of the currently accepted H⁺-dependent models (NHE, Na⁺ channel/V-type H⁺-ATPase), or co-transport schemes (NCC, NKCC), and ammonia excretion does not fit the current “Na⁺/NH₄ ⁺ exchange metabolon” paradigm. Na⁺, K⁺-ATPase and V-type H⁺-ATPase activities were present at similar levels in gill homogenates, Acute exposure to high environmental ammonia (NH₄Cl, 10^?3 M) significantly increased J _in ^Na , and NH₄ ⁺ was equally or more effective than K⁺ in activating branchial Na⁺,(K⁺) ATPase activity in vitro. We propose that ammonia excretion does not depend on Na⁺ uptake, but that Na⁺ uptake (by an as yet unknown H⁺-dependent apical mechanism) depends on ammonia excretion, driven by active NH₄ ⁺ entry via basolateral Na⁺,(K⁺)-ATPase.     

Salt accumulation and depletion in the root-zone of the halophyte Atriplex nummularia Lindl.: influence of salinity,leaf area and plant water use

Background and aims

Salt is known to accumulate in the root-zone of Na⁺ excluding glycophytes under saline conditions. We examined the effect of soil salinity on Na⁺ and Cl^? depletion or accumulation in the root-zone of the halophyte (Atriplex nummularia Lindl).

Methods

A pot experiment was conducted in soil to examine Na⁺ and Cl^? concentrations adjacent to roots at four initial NaCl treatments (20, 50, 200 or 400 mM NaCl in the soil solution). Plant water use was manipulated by leaving plants with all leaves intact, removing approximately 50 % of leaves, or removing all leaves. Daily evapotranspiration was replaced by watering undrained pots to weight with deionised water. After 35-38 days, samples were taken of the bulk soil and of soil loosely- and closely-adhering to the roots.

Results

In plants with leaves intact grown with 200 and 400 mM NaCl, average Na⁺ and Cl^? concentrations in the closely adhering soil were about twice the concentrations of the bulk soil. Ion accumulation increased with final leaf area and with cumulative transpiration over the duration of the trial. By contrast, in plants grown with the lowest salinity treatment (20 mM NaCl), Na⁺ and Cl^? concentrations decreased in the closely adhering soil with increasing leaf area and increasing cumulative water use.

Conclusions

Our data show that Na⁺ and Cl^? are depleted from the root-zone of A. nummularia at low salinity but accumulate in the root-zone at moderate to high salinity, and that the ions are drawn towards the plant in the transpiration stream.     

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water coordination on the structure and properties of l-histidine and zwitterionic l-histidine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of l-histidine is examined. The effect of metal ions (Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Ni²⁺, Cu²⁺ and Zn²⁺) and water on structures of His·M(H₂O)m, m = 0.1 complexes have been determined theoretically employing density functional theories using extended basis sets. Of the five stable complexes investigated the relative stability of the gas-phase complexes computed with DFT methods (with one exception of K⁺ systems) suggest metallic complexes of the neutral l-histidine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of l-histidine in the presence of the metal cations Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Ni²⁺, Cu²⁺ and Zn²⁺ were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to l-histidine is exhibited by the Cu²⁺ cation. The computed Gibbs energies ΔG are negative, span a rather broad energy interval (from ?130 to ?1,300 kJ/mol), and upon hydration are appreciably lowered.     

Ion transport in broad bean leaf mesophyll under saline conditions

Main conclusion

Salt stress reduces the ability of mesophyll tissue to respond to light. Potassium outward rectifying channels are responsible for 84 % of Na ⁺ induced potassium efflux from mesophyll cells. Modulation in ion transport of broad bean (Vicia faba L.) mesophyll to light under increased apoplastic salinity stress was investigated using vibrating ion-selective microelectrodes (the MIFE technique). Increased apoplastic Na⁺ significantly affected mesophyll cells ability to respond to light by modulating ion transport across their membranes. Elevated apoplastic Na⁺ also induced a significant K⁺ efflux from mesophyll tissue. This efflux was mediated predominately by potassium outward rectifying channels (84 %) and the remainder of the efflux was through non-selective cation channels. NaCl treatment resulted in a reduction in photosystem II efficiency in a dose- and time-dependent manner. In particular, reductions in Fv′/Fm′ were linked to K⁺ homeostasis in the mesophyll tissue. Increased apoplastic Na⁺ concentrations induced vanadate-sensitive net H⁺ efflux, presumably mediated by the plasma membrane H⁺-ATPase. It is concluded that the observed pump’s activation is essential for the maintenance of membrane potential and ion homeostasis in the cytoplasm of mesophyll under salt stress.     

K+-dependent 3H-d-glucose transport by hepatopancreatic brush border membrane vesicles of a marine shrimp

The effects of sodium, potassium, sugar inhibitors, and membrane potential on ³H-d-glucose uptake by hepatopancreatic epithelial brush border membrane vesicles (BBMV) of the Atlantic marine shrimp, Litopenaeus setiferus, were investigated. Brush border membrane vesicles were prepared using a MgCl₂/EGTA precipitation method and uptake experiments were conducted using a high speed filtration technique. ³H-d-Glucose uptake was stimulated by both sodium and potassium and these transport rates were almost doubled in the presence of an inside-negative-induced membrane potential. Kinetics of ³H-d-glucose influx were hyperbolic functions of both external Na⁺ or K⁺, and an induced membrane potential increased influx J _max and lowered K_m in both salts. ³H-d-Glucose influx versus [glucose] in both Na⁺ or K⁺ media also displayed Michaelis–Menten properties that were only slightly affected by induced membrane potential. Phloridzin was a poor inhibitor of 0.5 mM ³H-d-glucose influx, requiring at least 5 mM in NaCl and 10 mM in KCl to significantly reduce hexose transport. Several sugars (d-galactose, α-methyl-d-gluco-pyranoside, unlabeled d-glucose, d-fructose, and d-mannose) were used at 75 mM as potential inhibitors of 0.1 mM ³H-d-glucose influx. Only unlabeled d-glucose, d-fructose, and d-mannose significantly (p < 0.05) reduced labeled glucose transport. An additional experiment using increasing concentrations of d-mannose (0, 10, 25, 75, and 100 mM) showed this hexose to be an effective inhibitor of 0.1 mM ³H-d-glucose uptake at concentrations of 75 mM and higher. As a whole these results suggest that ³H-d-glucose transport by hepatopancreatic BBMV occurs by a carrier system that is able to use both Na⁺ and K⁺ as drivers, is enhanced by membrane potential, is relatively refractory to phloridzin, and is only inhibited by itself, d-fructose, and d-mannose. These properties are similar to those exhibited by the mammalian SLC5A9/SGLT4 transporter, suggesting that an invertebrate analogue of this protein may occur in shrimp.     

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the molecule-cation interaction between Na⁺ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO₂ bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO₂ bond upon complex formation, leading to the strengthened C-NO₂ bond and the possibly reduced explosive sensitivity.

l-leucine, l-methionine, and l-phenylalanine share a Na+/K+-dependent amino acid transporter in shrimp hepatopancreas

Hepatopancreatic brush border membrane vesicles (BBMV), made from Atlantic White shrimp (Litopenaeus setiferus), were used to characterize the transport properties of ³H-l-leucine influx by these membrane systems and how other essential amino acids and the cations, sodium and potassium, interact with this transport system. ³H-l-leucine uptake by BBMV was pH-sensitive and occurred against transient transmembrane concentration gradients in both Na⁺- and K⁺-containing incubation media, suggesting that either cation was capable of providing a driving force for amino acid accumulation. ³H-l-leucine uptake in NaCl or KCl media were each three times greater in acidic pH (pH 5.5) than in alkaline pH (pH 8.5). The essential amino acid, l-methionine, at 20 mM significantly (p < 0.0001) inhibited the 2-min uptakes of 1 mM ³H-l-leucine in both Na⁺- and K⁺-containing incubation media. The residual ³H-l-leucine uptake in the two media were significantly greater than zero (p < 0.001), but not significantly different from each other (p > 0.05) and may represent an l-methionine- and cation-independent transport system. ³H-l-leucine influxes in both NaCl and KCl incubation media were hyperbolic functions of [l-leucine], following the carrier-mediated Michaelis–Menten equation. In NaCl, ³H-l-leucine influx displayed a low apparent K _M (high affinity) and low apparent J _max, while in KCl the transport exhibited a high apparent K _M (low affinity) and high apparent J _max. l-methionine or l-phenylalanine (7 and 20 mM) were competitive inhibitors of ³H-l-leucine influxes in both NaCl and KCl media, producing a significant (p < 0.01) increase in ³H-l-leucine influx K _M, but no significant response in ³H-l-leucine influx J _max. Potassium was a competitive inhibitor of sodium co-transport with ³H-l-leucine, significantly (p < 0.01) increasing ³H-l-leucine influx K _M in the presence of sodium, but having negligible effect on ³H-l-leucine influx J _max in the same medium. These results suggest that shrimp BBMV transport ³H-l-leucine by a single l-methionine- and l-phenylalanine-shared carrier system that is enhanced by acidic pH and can be stimulated by either Na⁺ or K⁺ acting as co-transport drivers binding to shared activator sites.     

A theoretical investigation of the characteristics of hydrogen/halogen bonding interactions in dibromo-nitroaniline

In this work, computations of density functional theory (DFT) were carried out to investigate the nature of interactions in solid 2,6-dibromo-4-nitroaniline (DBNA). This system was selected to mimic the hydrogen/halogen bonding found within crystal structures as well as within biological molecules. DFT (M06-2X/6-311++G**) calculations indicated that the binding energies for different of interactions lie in the range between ?1.66 and ?9.77 kcal mol^?1. The quantum theory of atoms in molecules (QTAIM) was applied to provide more insight into the nature of these interactions. Symmetry-adapted perturbation theory (SAPT) analysis indicated that stability of the Br···Br halogen bonds is predicted to be attributable mainly to dispersion, while electrostatic forces, which have been widely believed to be responsible for these types of interactions, play a smaller role. Our results indicate that, for those nuclei participating in hydrogen/halogen bonding interactions, nuclear quadrupole resonance parameters exhibit considerable changes on going from the isolated molecule model to crystalline DBNA.

Ecosystem changes in Galápagos highlands by the invasive tree Cinchona pubescens

Background and aims

Salinity is an increasing problem for agricultural production worldwide. Understanding how Na⁺ enters plants is important if reducing Na⁺ influx, a key component of the regulation of Na⁺ accumulation in plants and improving salt tolerance of crop plants, is to be achieved. Our previous work indicated that two distinct low-affinity Na⁺ uptake pathways exist in the halophyte Suaeda maritima. Here, we report the external NaCl concentration at which uptake switches from pathway 1 to pathway 2 and the kinetics of the interaction between external K⁺ concentration and Na⁺ uptake and accumulation in S. maritima in order to determine the roles of K⁺ transporters or channels in low-affinity Na⁺ uptake.

Methods

Na⁺ influx, Na⁺ and K⁺ accumulations in S. maritima exposed to various concentrations of NaCl (0–200 mM) were analyzed in the absence and presence of the inhibitors TEA and Ba⁺ (5 mM TEA or 3 mM Ba²⁺) or KCl (0, 10 or 50 mM).

Results

Our earlier proposal was confirmed and extended that there are two distinct low-affinity Na⁺ uptake pathways in S. maritima: pathway 1 might be mediated by a HKT-type transporter under low salinity conditions and pathway 2 by an AKT1-type channel or a KUP/HAK/KT type transporter under high salinity conditions. The external NaCl concentration at which two distinct low-affinity Na⁺ uptake switches from pathway 1 to pathway 2, the ‘turning point’, is between 90 and 95 mM. Over a short period (12 h) of Na⁺ and K⁺ treatments, a low concentration of K⁺ (10 mM) facilitated Na⁺ uptake by S. maritima under high salinity (100–200 mM NaCl), whether or not the plants had been subjected to a longer (3 d) period of K⁺ starvation. The kinetics suggests that low concentration of K⁺ (10 mM) might activate AKT1-type channels or KUP/HAK/KT-type transporters under high salinity (100–200 mM NaCl).

Conclusions

The turning-point of external NaCl concentrations for the two low-affinity Na⁺ uptake pathways in Suaeda maritima is between 90 and 95 mM. A low concentration of K⁺ (10 mM) might activate AKT1 or KUP/HAK/KT and facilitate Na⁺ uptake under high salinity (100–200 mM NaCl). The kinetics of K⁺ on Na⁺ uptake and accumulation in S maritima are also consistent with there being two low-affinity Na⁺ uptake pathways.     

Purification, characterization and kinetic properties of extracellular l-asparaginase produced by Cladosporium sp.

l-asparaginase from Cladosporium sp. grown on wheat bran by SSF was purified. Enzyme appeared to be a trimer with homodimer of 37 kDa and another 47 kDa amounting to total mass of 121 kDa as estimated by SDS-PAGE and 120 kDa on gel filtration column. The optimum temperature and pH of the enzyme were 30 °C and 6.3, respectively with Vmax of 4.44 μmol/mL/min and Km of 0.1 M. Substrate specificity studies indicated that, l-asparaginase has greater affinity towards l-asparagine with substrate hydrolysis efficiency (Vmax/Km ratio) eightfold higher than that of l-glutamine. l-asparaginase activity in presence of thiols studied showed decrease in Vmax and increase in Km, indicating nonessential mode of inactivation. Among the thiols tested, β-mercaptomethanol, exerted inhibitory effect, suggesting a critical role of disulphide linkages in maintaining a suitable conformation of the enzyme. Metal ions such as Ca²⁺, Co²⁺, Cu²⁺, Mg²⁺, Na⁺, K⁺ and Zn²⁺ significantly affected enzyme activity whereas presence of Fe³⁺, Pb²⁺ and KI stimulated the activity. Detergents studied also enhanced l-asparaginase activity. In-vitro half-life of purified l-asparaginase in mammalian blood serum was 93.69 h. The enzyme inhibited acrylamide formation in potato chips by 96 % making it a potential candidate for food industry to reduce acrylamide content in starchy fried food commodities.     

Transport of l-proline by the proton-coupled amino acid transporter PAT2 in differentiated 3T3-L1 cells

Mechanism and substrate specificity of the proton-coupled amino acid transporter 2 (PAT2, SLC36A2) have been studied so far only in heterologous expression systems such as HeLa cells and Xenopus laevis oocytes. In this study, we describe the identification of the first cell line that expresses PAT2. We cultured 3T3-L1 cells for up to 2 weeks and differentiated the cells into adipocytes in supplemented media containing 2 μM rosiglitazone. During the 14 day differentiation period the uptake of the prototype PAT2 substrate l-[³H]proline increased ~5-fold. The macro- and microscopically apparent differentiation of 3T3-L1 cells coincided with their H⁺ gradient-stimulated uptake of l-[³H]proline. Uptake was rapid, independent of a Na⁺ gradient but stimulated by an inwardly directed H⁺ gradient with maximal uptake occurring at pH 6.0. l-Proline uptake was found to be mediated by a transport system with a Michaelis constant (K_t) of 130 ± 10 μM and a maximal transport velocity of 4.9 ± 0.2 nmol × 5 min^?1 mg of protein^?1. Glycine, l-alanine, and l-tryptophan strongly inhibited l-proline uptake indicating that these amino acids also interact with the transport system. It is concluded that 3T3-L1 adipocytes express the H⁺-amino acid cotransport system PAT2.     

Effect of Vanadium on the Subset and Proliferation of Peripheral Blood T Cells, and Serum Interleukin-2 Content in Broilers

The purpose of this 42-day study was to investigate the effects of dietary excess vanadium on immune function by determining changes of the subsets and proliferation function of peripheral blood T cells. Four hundred twenty 1-day-old avian broilers were divided into six groups and fed on a corn–soybean basal diet as control diet or the same diet amended to contain 5, 15, 30, 45, and 60 ppm vanadium supplied as ammonium metavanadate. In comparison with those of the control group, the percentages of CD ₃ ⁺ , CD ₃ ⁺ CD ₄ ⁺ , and CD ₃ ⁺ CD ₈ ⁺ were decreased in 45 and 60 ppm groups from 14 to 42 days of age, and the percentages of CD ₃ ⁺ and CD ₃ ⁺ CD ₄ ⁺ were increased in 5 ppm group at 42 days of age. The CD ₄ ⁺ /CD ₈ ⁺ ratio was increased in 45 and 60 ppm groups at 28 days of age. Meanwhile, the proliferation function of peripheral blood T cell were decreased in 30, 45, and 60 ppm groups from 14 to 42 days of age. Also, the serum interleukin-2 contents were decreased in 45 and 60 ppm groups from 14 to 42 days of age and increased in 5 ppm group at 28 days of age. Histopathologically, hypocellularity appeared in the thymus in 45 and 60 ppm groups. It was concluded that dietary vanadium in excess of 30 ppm reduced the percentages of peripheral blood T-cell subsets and the proliferation function and serum interleukin-2 contents. The cellular immune function was finally impaired in broilers.     

Non-covalent interactions – QTAIM and NBO analysis

MP2(full)/6-311++G(3df,3pd) calculations were carried out on complexes linked through various non-covalent Lewis acid – Lewis base interactions. These are: hydrogen bond, dihydrogen bond, hydride bond and halogen bond. The quantum theory of ´atoms in molecules´ (QTAIM) as well as the natural bond orbitals (NBO) method were applied to analyze properties of these interactions. It was found that for the A-H…B hydrogen bond as well as for the A-X…B halogen bond (X designates halogen) the complex formation leads to the increase of s-character in the A-atom hybrid orbital aimed toward the H or X atom. In opposite, for the A…H-B hydride bond, where the H-atom possesses negative charge, the decrease of s-character in the B-atom orbital is observed. All these changes connected with the redistribution of the electron charge being the effect of the complex formation are in line with Bent´s rule. The numerous correlations between energetic, geometrical, NBO and QTAIM parameters were also found.

Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube

The dynamics of Na⁺ transportation in a transmembrane cyclic peptide nanotube of 8?×?(WL)₄/POPE has been simulated. The curve of PMF (potential of mean force) for Na⁺ moving through the tube, based on ABF (adaptive biasing force) method, indicates that Na⁺ possesses lower free energy in an α-plane region than in a mid-plane one. It was found that Na⁺ would desorb one or two water molecules in the first solvation shell when entering the tube and later maintain in a solvation state. The average numbers of water molecules around Na⁺ are 4.50, 4.09 in the first solvation shell, and 3.10, 4.08 in the second one for Na⁺ locating in an α-plane zone and a mid-plane region, respectively. However, water molecules far away from Na⁺ location still nearly arrange in a form of 1-2-1-2 file. The dipole orientations of water molecules in the regions of gaps 1 and 7 display “D-defects”, resulted from the simultaneous electrostatic potentials generated by Na⁺ and the bare carbonyls at the tube mouths. Such “D-defects” accommodate the energetically favorable water orientations thereby.

Presence of a Na+/H+ antiporter in Methanobacterium thermoautotrophicum and its role in Na+ dependent methanogenesis

Methane formation from H₂/CO₂ by methanogenic bacteria is dependent on Na⁺ ions. In this communication it is shown with Methanobacterium thermoautotrophicum that a Na⁺/H⁺ antiporter plays a role in methane formation from H₂ and CO₂ and in the regulation of the ΔpH. This is based on the following findings:

1. Li⁺ ions, an alternative substrate of Na⁺/H⁺ antiporters, could replace Na⁺ in stimulating methanogenesis from H₂ and CO₂.
2. Harmaline, amiloride, and NH ₄ ⁺ , which are inhibitors of Na⁺/H⁺ antiporters, inhibited methanogenesis; inhibition was competitive to Na⁺ or Li⁺.
3. Addition of Na⁺ or Li⁺ rather than of other cations to cell suspensions resulted in an acidification of the suspension medium. The rate and extent of acidification was affected by those inhibitors, which inhibited methanogenesis competitively to Na⁺ or Li.
4. During methane formation from H₂ and CO₂ the generation of a ΔpH (inside alkaline) was dependent on the presence of Na⁺ or Li⁺. However, methanogenesis was also dependent on Na⁺ or Li⁺ under conditions where ΔpH was zero.
5. ATP synthesis driven by an electrogenic potassium efflux was significantly enhanced in the presence of Na⁺ or Li⁺. Na⁺ or Li⁺ were shown to prevent acidification of the cytoplasm under these conditions.

     

Optical chemosensors for Cu(II) ion based on BODIPY derivatives: an experimental and theoretical study

Two BODIPY derivatives for Cu²⁺ ion chemosensors containing 4-[2-(diethylamino)-2-oxoethoxy]phenyl (BDP1) and 3,4-bis[2-(diethylamino)-2-oxoethoxy]phenyl (BDP2) were synthesized by coupling appropriate N,N-diethyl-2-(4-formylphenoxy)acetamide and 2,4-dimethylpyrrole moieties in the presence of trifluoroacetic acid and anhydrous dichloromethane at room temperature. The binding abilities between these chemosensors and 50 equivalents of Na⁺, K⁺, Ag⁺, Ca²⁺, Fe²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, Hg²⁺ and Pb²⁺ ions were studied using UV-vis and fluorescence spectrophotometry. The results show that, compared to other ions, both the UV-vis absorption and fluorescence emission intensity of BDP2 decreased dramatically when Cu²⁺ ion was added. To explain this behavior, ab initio quantum chemical calculations were performed using correlated second-order Møller-Plesset perturbation theory (MP2/LanL2DZ). The calculated orbital energies indicated that the decrease in UV-vis absorption intensity and the quenching of fluorescene emission were due to the single-electron reduction of Cu²⁺ to Cu⁺ ion.