Ligation of Aza bases to the AgF<Subscript>2</Subscript> molecule: a theoretical study

We have analyzed the electronic structure and chemical bonding for molecular adducts of the Ag(II)F₂ molecule with various aza Lewis bases including ammonia, nitriles, secondary amines, and their derivatives exhibiting various degrees of fluorination. Density functional theory calculations indicate that a progressive shift occurs of the spin density from the Ag center towards the coordinating nitrogen atoms of aza ligands, as the ligation energy increases. Chemistry of Ag(II) might be extended with little effort beyond the known aza connections, to include nitriles, perfluorinated nitriles and perfluorinated amines. Figure Properties of a variety of novel adducts of the AgF₂ molecule with two aza bases (L), possible precursors of the AgF₂L₂ extended solids, were assessed by the DFT calculations Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. This work is dedicated to memory of Wojciech Ochmański, unforgettable person, good-hearted man, whose craftsmanship in work was second-to-none.     

TCNE-modified graphene as an adsorbent for N<Subscript>2</Subscript>O molecule: a DFT study

Adsorption behavior of nitrous oxide (N₂O) on pristine graphene (PG) and tetracyanoethylene (TCNE) modified PG surfaces is investigated using density functional theory. A number of initial adsorbate geometries are considered on both surfaces and the most stable ones are chosen upon calculation of the adsorption energies (E_ads). N₂O is found to adsorb in a weakly exoergic process (E_ads?～??3.18 kJ mol^?1) at the equilibrium distance of 3.52 Å on the PG surface. N₂O adsorption can be greatly enhanced with the presence of a TCNE molecule (E_ads?=??87.00 kJ mol^?1). Mulliken charge analysis confirms that adsorption of N₂O is not accompanied by distinct charge transfer from the surfaces to the molecule (? 0.001 │e│ for each case). Moreover, on the basis of calculated changes in the HOMO/LUMO energy gap, it is found that electronic properties of PG and TCNE modified PG are not sensitive toward adsorption of N₂O, indicating that both surfaces are not good enough to introduce as an N₂O detector. However, the considerable amount of E_ads in TCNE modified PG can be a guide to the design of graphene-based adsorbents for N₂O capture.     

Mechanistic insights into C-H activation from radical clock chemistry: oxidation of substituted methylcyclopropanes catalyzed by soluble methane monooxygenase from Methylosinus trichosporium OB3b

The soluble methane monooxygenase (MMO) system isolated from Methylosinus trichosporium OB3b catalyzes the adventitious oxidation of alkyl substituted methylcyclopropanes. If the chemical mechanism of C-H activation by MMO involves formation of a radical or carbocation intermediate at the methyl C-H of these 'radical clock' substrates, then cyclopropyl ring opened alcohols may appear in the product mixture due to rearrangement of the intermediate. The lifetime of radical intermediates can be determined from known rearrangement rate constants, k(r). Rearrangement was observed during the oxidation of 1,1,2,2-tetramethylcyclopropane (k(r)=1.7-17. 5x10(8) s(-1), 30 degrees C) but not for cis- or trans-1, 2-dimethylcyclopropane (k(r)=1.2-6.4x10(8) s(-1), 30 degrees C) or the very fast radical clock, trans-2-phenylmethylcyclopropane (k(r)=3.4x10(11) s(-1), 30 degrees C). The results show that the occurrence of rearranged products fails to correlate with either the chemical nature of the C-H bond being broken, which is very similar for all of the methylcyclopropanes studied here, or the magnitude of the radical k(r) value. This study suggests that the steric properties of the substrate play an important role in determining the outcome of the reaction. Substrates with bulky substituents near the C-H bond that is attacked appear to yield intermediates with sufficient lifetimes to rearrange. In contrast, substrates with less steric bulk are postulated to be able to approach the reactive oxygen species in the MMO active site more closely so that intermediates are either rapidly quenched or undergo subsequent interaction with the dinuclear iron cluster of MMO that prevents rearrangement.     

An investigation into possible quantum chaos in the H<Subscript>2</Subscript> molecule under intense laser fields via Ehrenfest phase space (EPS) trajectories

By employing the Ehrenfest "phase space" trajectory method for studying quantum chaos, developed in our laboratory, the present study reveals that the H₂ molecule under intense laser fields of three different intensities, I?=?1?×?10¹⁴ W/cm², 5?×?10¹⁴ W/cm², and 1?×?10¹⁵ W/cm², does not show quantum chaos. A similar conclusion is also reached through the Loschmidt echo (also called quantum fidelity) calculations reported here for the first time for a real molecule under intense laser fields. Thus, a long-standing conjecture about the possible existence of quantum chaos in atoms and molecules under intense laser fields has finally been tested and not found to be valid in the present case.     

Neuroprotection by adenosine in the brain: From A<Subscript>1</Subscript> receptor activation to A<Subscript>2A</Subscript> receptor blockade

Adenosine is a neuromodulator that operates via the most abundant inhibitory adenosine A₁ receptors (A₁Rs) and the less abundant, but widespread, facilitatory A_2ARs. It is commonly assumed that A₁Rs play a key role in neuroprotection since they decrease glutamate release and hyperpolarize neurons. In fact, A₁R activation at the onset of neuronal injury attenuates brain damage, whereas its blockade exacerbates damage in adult animals. However, there is a down-regulation of central A₁Rs in chronic noxious situations. In contrast, A_2ARs are up-regulated in noxious brain conditions and their blockade confers robust brain neuroprotection in adult animals. The brain neuroprotective effect of A_2AR antagonists is maintained in chronic noxious brain conditions without observable peripheral effects, thus justifying the interest of A_2AR antagonists as novel protective agents in neurodegenerative diseases such as Parkinsons and Alzheimers disease, ischemic brain damage and epilepsy. The greater interest of A_2AR blockade compared to A₁R activation does not mean that A₁R activation is irrelevant for a neuroprotective strategy. In fact, it is proposed that coupling A_2AR antagonists with strategies aimed at bursting the levels of extracellular adenosine (by inhibiting adenosine kinase) to activate A₁Rs might constitute the more robust brain neuroprotective strategy based on the adenosine neuromodulatory system. This strategy should be useful in adult animals and especially in the elderly (where brain pathologies are prevalent) but is not valid for fetus or newborns where the impact of adenosine receptors on brain damage is different.     

Elevated CO<Subscript>2</Subscript>, litter chemistry,and decomposition: a synthesis

The results of published and unpublished experiments investigating the impacts of elevated [CO₂] on the chemistry of leaf litter and decomposition of plant tissues are summarized. The data do not support the hypothesis that changes in leaf litter chemistry often associated with growing plants under elevated [CO₂] have an impact on decomposition processes. A meta-analysis of data from naturally senesced leaves in field experiments showed that the nitrogen (N) concentration in leaf litter was 7.1% lower in elevated [CO₂] compared to that in ambient [CO₂]. This statistically significant difference was: (1) usually not significant in individual experiments, (2) much less than that often observed in green leaves, and (3) less in leaves with an N concentration indicative of complete N resorption. Under ideal conditions, the efficiency with which N is resorbed during leaf senescence was found not to be altered by CO₂ enrichment, but other environmental influences on resorption inevitably increase the variability in litter N concentration. Nevertheless, the small but consistent decline in leaf litter N concentration in many experiments, coupled with a 6.5% increase in lignin concentration, would be predicted to result in a slower decomposition rate in CO₂-enriched litter. However, across the assembled data base, neither mass loss nor respiration rates from litter produced in elevated [CO₂] showed any consistent pattern or differences from litter grown in ambient [CO₂]. The effects of [CO₂] on litter chemistry or decomposition were usually smallest under experimental conditions similar to natural field conditions, including open-field exposure, plants free-rooted in the ground, and complete senescence. It is concluded that any changes in decomposition rates resulting from exposure of plants to elevated [CO₂] are small when compared to other potential impacts of elevated [CO₂] on carbon and N cycling. Reasons for experimental differences are considered, and recommendations for the design and execution of decomposition experiments using materials from CO₂-enrichment experiments are outlined.     

Mechanistic Insight into the H<Subscript>2</Subscript>O/D<Subscript>2</Subscript>O Isotope Effect in the Proton Transport of the Influenza Virus M2 Protein

The M2 proton channel is essential for the replication of the flu virus and is a known drug target. The functional mechanism of channel activation and conductance is key to both the basic biology of viral replication and the design of drugs that can withstand mutations. A quantitative model was previously developed for calculating the rate of proton transport through the M2 channel. The permeant proton was assumed to diffuse to the pore, obligatorily bind to the His37 tetrad, and then dissociate and be released to either side of the tetrad. Here the model is used to calculate the effect of a change in solvent from H₂O to D₂O on the rate of proton transport. The solvent substitution affects two parameters in the model: the proton diffusion constant and the pK _a for proton binding to the His37 tetrad. When the known effects on these two parameters are included, the deuterium isotope effect calculated from the model is in quantitatively agreement with experimental results. This strict test of the theoretical model provides strong support for the hypothesis that the permeant proton obligatorily binds to and then unbinds from the His37 tetrad. This putatively essential role of the His37 tetrad in the functional mechanism of the M2 channel makes it a promising target for designing mutation-tolerant drugs.     

The platinum-olefin binding energy in series of (PH<Subscript>3</Subscript>)<Subscript>2</Subscript>Pt(olefin) complexes - a theoretical study

Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics bearing coordinated olefins with general formula (R¹R²C = CR³R⁴)Pt(PH₃)₂ [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin substituents. Figure Representation of (CH₂ = CHR)Pt(PPh₃)₂ and the stability chart     

Differential gene expression during apoptosis induced by a serum factor: Role of mitochondrial F<Subscript>0</Subscript>-F<Subscript>1</Subscript> ATP synthase complex

The number of genes that are up regulated or down regulated during apoptosis is large and still increasing. In an attempt to characterize differential gene expression during serum factor induced apoptosis in AK-5 cells (a rat histiocytoma), we found subunit 6 and subunit 8 of the transmembrane proton channel and subunit alpha of the catalytic core of the mitochondrial F₀-F₁ ATP synthase complex to be up regulated during apoptosis. The increase in the expression levels of these subunits was concomitant with a transient increase in the intracellular ATP levels, suggesting that the increase in cellular ATP content is a result of the increase in the expression of ATP synthase subunits' gene and de novo protein synthesis. Depleting the cellular ATP levels with oligomycin inhibited apoptosis significantly, pointing to the requirement of ATP during apoptosis. Caspase 1 and caspase 3 activity and the loss of mitochondrial membrane potential were also inhibited by oligomycin during apoptosis in these cells, suggesting that the oligomycin induced inhibition of apoptosis could be due to inhibition of caspase activity and inhibition of mitochondrial depolarization. However, cytochrome C release during apoptosis was found to be completely independent of intracellular ATP content. Besides the ATP synthase complex genes, other mitochondrial genes like cytochrome C oxidase subunit II and III also showed elevated levels of expression during apoptosis. This kind of a mitochondrial gene expression profile suggests that in AK-5 cells, these genes are upregulated in a time-linked manner to ensure sufficient intracellular ATP levels and an efficient functioning of the mitochondrial respiratory chain for successful completion of the apoptotic pathway.     

Nitrosation of malononitrile by HONO,ClNO and N<Subscript>2</Subscript>O<Subscript>3</Subscript>: A theoretical study

Nitrosation reactions of malononitrile by three nitrosating agents, HONO, ClNO, and N₂O₃, have been theoretically investigated at the B3LYP/cc-pVTZ and MP2/cc-pVDZ levels. Two possible competitive paths for nitrosation of malononitrile to give 2-nitroso-malononitrile were proposed: (a) direct C-nitrosation and (b) N-nitrosation and subsequent nitroso transfer from N to C atom. The calculations show that at both B3LYP and MP2 levels, path b is kinetically favored over path a for nitrosations by HONO and N₂O₃. In the case of ClNO, the B3LYP predicts preference of path b, while the MP2 calculations suggest that both paths have similar rate-determining barriers. The data suggest that N₂O₃ is the preferred nitrosating agent for the nitrosation of malononitrile in aqueous solution. Transformation of 2-nitroso-malononitrile to form malononitrileoxime via intramolecular proton transfer has also been explored, and it is found that inclusion of an assistant water molecule can drastically accelerate the tautomerization.     

Study of Plasma Induced Chemistry by DC Discharges in CO<Subscript>2</Subscript>/N<Subscript>2</Subscript>/H<Subscript>2</Subscript>O Mixtures Above a Water Surface

The chemistry induced by atmospheric pressure DC discharges above a water surface in CO(2)/N(2)/H(2)O mixtures was investigated. The gaseous mixtures studied represent a model prebiotic atmosphere of the Earth. The most remarkable changes in the chemical composition of the treated gas were the decomposition of CO(2) and the production of CO. The concentration of CO increased logarithmically with the increasing input energy density and an increasing initial concentration of CO(2) in the gas. The highest achieved concentration of CO was 4.0 +/- 0.6 vol. %. The production of CO was crucial for the synthesis of organic species, since reactions of CO with some reactive species generated in the plasma, e. g. H* or N* radicals, were probably the starting point in this synthesis. The presence of organic species (including the tentative identification of some amino acids) was demonstrated by the analysis of solid and liquid samples by high-performance liquid chromatography, infrared absorption spectroscopy and proton-transfer-reaction mass spectrometry. Formation of organic species in a completely inorganic CO(2)/N(2)/H(2)O atmosphere is a significant finding for the theory of the origins of life.     

Implications of interveinal distance for quantum yield in C<Subscript>4</Subscript> grasses: a modeling and meta-analysis

The distance between veins has the potential to affect photosynthesis in C₄ grasses because photon capture and photosynthetic carbon reduction are primarily restricted to vascular bundle sheath cells (BSC). For example, BSC density should increase as interveinal distance (IVD) decreases, and thus IVD may influence photon capture and photosynthesis in C₄ grasses. The objective of this study is to evaluate the potential importance of IVD to the function of C₄ grasses, and a literature survey is conducted to test the hypothesis that quantum yield of photosynthesis () increases with decreasing IVD. First, a meta-analysis of and IVD values obtained for 12 C₄ grass species supports this hypothesis as and IVD are significantly negatively correlated (r=–0.61). Second, a regression of carbon isotope discrimination () versus IVD was conducted and the regression equation was used in a simple biochemical model that relates to and leakage of CO₂ from the BSC. The modeling analysis also supports the hypothesis that decreases with increasing IVD in C₄ grasses. C₄ grasses are virtually absent from shaded habitats, and the biochemical model is employed to examine the implications of IVD for shade-tolerance in C₄ grasses. The model predicts that only those species with uncommonly small IVD values are able to tolerate prolonged shade.     

The polythiophene molecular segment as a sensor model for H<Subscript>2</Subscript>O,HCN, NH<Subscript>3</Subscript>, SO<Subscript>3</Subscript>, and H<Subscript>2</Subscript>S: a density functional theory study

Studying the interaction of some atmospheric gases (H₂O, HCN, NH₃, SO₃ and H₂S) with 3PT oligomers is important in the development of polymeric sensors for gas detection. In the present study, we studied the relaxed geometries, interaction energies, charge analysis, HOMO–LUMO orbital analysis, and UV–vis spectra of all interacted systems using first-principles density functional theory (DFT). All these analyses indicated the potential of polythiophene as an inexpensive polymeric sensor for the analytes mentioned. Interaction energy values of ?19.90, ?19.66, ?14.01, ?8.70, and ?4.76 kJ mol^?1 were achieved for adsorption of SO₃, H₂O, NH₃, HCN, and H₂S on 3PT, respectively. Consequently, clarification of their physical parameters became the major focus of this study.     

Bioactive M(II) complexes of amino acid-based N<Subscript>3</Subscript>O donor mixed ligand: in vitro and in silico DNA binding studies

Three novel mixed ligand M(II) complexes, namely [CoL¹L²Cl₂] (1), [CuL¹L²Cl₂] (2), and [ZnL¹L²Cl₂] (3), were synthesized using 1,4-naphthoquinone, L-histidine, and 1,10-phenanthroline as ligands. The ligand framework and the corresponding structural changes on complexation were ascertained based on the results of elemental analysis, conductivity measurements, magnetic behavior, FT-IR, UV-visible, ¹H NMR, ¹³C NMR, ESR spectral studies, and ESI mass spectrometry. The biological action of the ligand (L) and complexes 1–3 such as DNA binding and cleaving ability were studied. Results suggest that the ligand and the complexes could interact with calf thymus-DNA (CT-DNA) via intercalation mode. Additionally, complex 2 displayed potential antioxidant activity in in vitro studies. Docking simulation was performed to position the ligand and the complexes into the active site of BDNA (IBNA) to determine the probable binding mode.     

Insight into the lithium/hydrogen bonding in (CH<Subscript>2</Subscript>)<Subscript>2</Subscript>X...LiY/HY (X: C=CH<Subscript>2</Subscript>, O,S; Y=F,Cl, Br) complexes

The nature of the lithium/hydrogen bonding between (CH₂)₂X(X: C=CH₂, O, S) and LiY/HY(Y=F, Cl, Br) have been theoretically investigated at MP2/6-311++G (d, p) level, using Bader’s “atoms in molecules (AIM)” theory and Weinhold’s “natural bond orbital (NBO)” methodology. The molecule formation density differences (MFDD) of the titled complexes are analyzed. Two kinds of geometries of the lithium/hydrogen bonded complexes are compared. As a whole, the nature of lithium bond and hydrogen bond are different. For the same electron donor and the same acceptor, lithium bond is stronger than hydrogen bond. For the same electron acceptor and different kind of donors, the interaction energies follows the n-type> π-type > pseudo-π-type order. For the same (CH₂)₂X, the interaction energy increases in the sequence of Y=F, Cl and Br for lithium bond systems while it decreases for hydrogen bond systems. Electron transfer plays an important role in the formation of lithium bond systems while it is less important in the hydrogen bond systems.     

Elevated CO<Subscript>2</Subscript> ameliorated oxidative stress induced by elevated O<Subscript>3</Subscript> in <Emphasis Type="Italic">Quercus mongolica</Emphasis>

Using open top chambers, the effects of elevated O₃ (80 nmol mol⁻¹) and elevated CO₂ (700 μmol mol⁻¹), alone and in combination, were studied on young trees of Quercus mongolica. The results showed that elevated O₃ increased malondialdehyde content and decreased photosynthetic rate after 45 days of exposure, and prolonged exposure (105 days) induced significant increase in electrolyte leakage and reduction of chlorophyll content. All these changes were alleviated by elevated CO₂, indicating that oxidative stress on cell membrane and photosynthesis was ameliorated. After 45 days of exposure, elevated O₃ stimulated activities of superoxide dismutase (SOD, EC 1.15.1.1) and ascorbate peroxidase (APX, EC 1.11.1.11), but the stimulation was dampened under elevated CO₂ exposure. Furthermore, ascorbate (AsA) and total phenolics contents were not higher in the combined gas treatment than those in elevated O₃ treatment. It indicates that the protective effect of elevated CO₂ against O₃ stress was achieved hardly by enhancing ROS scavenging ability after 45 days of exposure. After 105 days of exposure, elevated O₃ significantly decreased activities of SOD, catalase (CAT, EC 1.11.1.6) and APX and AsA content. Elevated CO₂ suppressed the O₃-induced decrease, which could ameliorate the oxidative stress in some extent. In addition, elevated CO₂ increased total phenolics content in the leaves both under ambient O₃ and elevated O₃ exposure, which might contribute to the protection against O₃-induced oxidative stress as well.     

O<Subscript>2</Subscript> consumption rates along the growth curve: new insights into <Emphasis Type="BoldItalic">Trypanosoma cruzi</Emphasis> mitochondrial respiratory chain

Understanding the energy-transduction pathways employed by Trypanosoma cruzi, the etiological agent of Chagas disease, may lead to the identification of new targets for development of a more effective therapy. Herein, the contribution of different substrates for O₂ consumption rates along T. cruzi epimastigotes (Tulahuen 2 and Y strains) growth curve was evaluated. O₂ consumption rates were higher at the late stationary phase not due to an increase on succinate-dehydrogenase activity. Antimycin A and cyanide did not totally inhibit the mitochondrial respiratory chain (MRC). Malonate at 10 or 25 mM was not a potent inhibitor of complex II. Comparing complex II and III, the former appears to be the primary site of H₂O₂ release. An update on T. cruzi MRC is presented that together with our results bring important data towards the understanding of the parasite’s MRC. The findings mainly at the stationary phase could be relevant for epimastigotes transformation into the metacyclic form, and in this sense deserves further attention.