Theoretical investigations of a high density cage compound 10-(1-nitro-1, 2, 3, 4-tetraazol-5-yl)) methyl-2, 4, 6, 8, 12-hexanitrohexaazaisowurtzitane

A new polynitro cage compound with the framework of HNIW and a tetrazole unit, i.e., 10-(1-nitro-1, 2, 3, 4-tetraazol-5-yl)) methyl-2, 4, 6, 8, 12-hexanitrohexaazaisowurtzitane (NTz-HNIW) has been proposed and studied by density functional theory (DFT) and molecular mechanics methods. Properties such as IR spectrum, heat of formation, thermodynamic properties, and crystal structure were predicted. The compound belongs to the Pbca space group, with the lattice parameters a = 15.07 ?, b = 12.56 ?, c = 18.34 ?, Z = 8, and ρ = 1.990 g·cm^-3. The stability of the compound was evaluated by the bond dissociation energies and results showed that the first step of pyrolysis is the rupture of the N–NO₂ bond in the side chain. The detonation properties were estimated by the Kamlet-Jacobs equations based on the calculated crystal density and heat of formation, and the results were 9.240 km·s^-1 for detonation velocity and 40.136 GPa for detonation pressure. The designed compound has high thermal stability and good detonation properties and is probably a promising high energy density compound (HEDC).     

Density functional theory study of the potassium complexation of an unsymmetrical 1,3-alternate calix[4]-crown-5-N-azacrown-5 bearing two different crown rings

Theoretical studies of an unsymmetrical calix[4]-crown-5-N-azacrown-5 (1) in a fixed 1,3-alternate conformation and the complexes 1·K⁺(a), 1·K⁺(b), 1·K⁺(c) and 1·K⁺K⁺ were performed using density functional theory (DFT) at the B3LYP/6-31G* level. The fully optimized geometric structures of the free macroligand and its 1:1 and 1:2 complexes, as obtained from DFT calculations, were used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal–ligand and cation–π interactions were investigated. NBO analysis indicated that the stabilization interaction energies (E ₂) for O…K⁺ and N…K⁺ are larger than the other intermolecular interactions in each complex. The significant increase in electron density in the RY* or LP* orbitals of K⁺ results in strong host–guest interactions. In addition, the intermolecular interaction thermal energies (ΔE, ΔH, ΔG) were calculated by frequency analysis at the B3LYP/6-31G* level. For all structures, the most pronounced changes in the geometric parameters upon interaction are observed in the calix[4]arene molecule. The results indicate that both the intermolecular electrostatic interactions and the cation–π interactions between the metal ion and π orbitals of the two pairs that face the inverted benzene rings play a significant role.     

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.     

The Interactions of Glutathione-Capped CdTe Quantum Dots with Trypsin

Due to their unique fluorescent properties, quantum dots present a great potential for biolabelling applications; however, the toxic interactions of quantum dots with biopolymers are little known. The toxic interactions of glutathione-capped CdTe quantum dots with trypsin were studied in this paper using synchronous fluorescence spectroscopy, fluorescence emission spectra, and UV–vis absorption spectra. The interaction between CdTe quantum dots and trypsin resulted in structure changes of trypsin and inhibited trypsin's activity. Fluorescence emission spectra revealed that the quenching mechanism of trypsin by CdTe quantum dots was a static quenching process. The binding constant and the number of binding sites at 288 and 298 K were calculated to be 1.98 × 10⁶ L mol⁻¹ and 1.37, and 6.43 × 10⁴ L mol⁻¹ and 1.09, respectively. Hydrogen bonds and van der Waals' forces played major roles in this process.     

Plasma free amino acid kinetics in rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) using a bolus injection of <Superscript>15</Superscript>N-labeled amino acids

To gain insight into the metabolic design of the amino acid carrier systems in fish, we injected a bolus of ¹⁵N amino acids into the dorsal aorta in mature rainbow trout (Oncorhynchus mykiss). The plasma kinetic parameters including concentration, pool size, rate of disappearance (R _d), half-life and turnover rate were determined for 15 amino acids. When corrected for metabolic rate, the R _d values obtained for trout for most amino acids were largely comparable to human values, with the exception of glutamine (which was lower) and threonine (which was higher). R _d values ranged from 0.9 μmol 100 g⁻¹ h⁻¹ (lysine) to 22.1 μmol 100 g⁻¹ h⁻¹ (threonine) with most values falling between 2 and 6 μmol 100 g⁻¹ h⁻¹. There was a significant correlation between R _d and the molar proportion of amino acids in rainbow trout whole body protein hydrolysate. Other kinetic parameters did not correlate significantly with whole body amino acid composition. This indicates that an important design feature of the plasma-free amino acids system involves proportional delivery of amino acids to tissues for protein synthesis.     

Biodegradation kinetics of 1,4-benzoquinone in batch and continuous systems

Combining chemical and biological treatments is a potentially economic approach to remove high concentration of recalcitrant compounds from wastewaters. In the present study, the biodegradation of 1,4-benzoquinone, an intermediate compound formed during phenol oxidation by chlorine dioxide, was investigated using Pseudomonas putida (ATCC 17484) in batch and continuous bioreactors. Batch experiments were conducted to determine the effects of 1,4-benzoquinone concentration and temperature on the microbial activity and biodegradation kinetics. Using the generated data, the maximum specific growth rate and biodegradation rate were determined as 0.94 h⁻¹ and 6.71 mg of 1,4-benzoquinone l⁻¹ h⁻¹. Biodegradation in a continuous bioreactor indicated a linear relationship between substrate loading and biodegradation rates prior to wash out of the cells, with a maximum biodegradation rate of 246 mg l⁻¹ h⁻¹ observed at a loading rate of 275 mg l⁻¹ h⁻¹ (residence time: 1.82 h). Biokinetic parameters were also determined using the steady state substrate and biomass concentrations at various dilution rates and compared to those obtained in batch cultures.     

Scaling-up technique for net ecosystem productivity of deciduous broadleaved forests in Japan using MODIS data

We attempted to obtain carbon sequestration maps of deciduous forests in Japan using detectable parameters from the Moderate Resolution Imaging Spectrometer (MODIS) sensor and to determine how the spatial pattern of carbon sequestration differs within the same forest ecosystem type. For this investigation, we firstly parameterized the MODIS algorithm at one flux tower site, Takayama, for the years 2002–2003. The MODIS algorithm could link flux-based net ecosystem productivity (NEP) with simple functions controlled by a thermal infrared band and a vegetation index. Second, the performance of the MODIS algorithm was validated through comparisons with the flux-based NEP at another flux tower site, Hitsujigaoka. The MODIS-based NEP at Hitsujigaoka was also within an accuracy of a flux-based NEP with R ² of 0.879 and root mean square error of 1.64 gC m⁻² day⁻¹, regardless of canopy structure and age. The MODIS algorithm was noteworthy for its general applicability in different locations. Finally, we used the MODIS algorithm for the same forest ecosystem type in Japan for regional extrapolation of NEP. The MODIS-based NEP of deciduous forests in Japan showed great variance with 347 ± 288 gC m⁻² year⁻¹ in 2002, according to the stand structure and climatic condition of the year. Studies for quantification of ecosystem carbon balance need to consider variance, frequency and spatial distributions of NEP. Satellite remote sensing demonstrated the potential for the large-scale mapping of NEP.     

Molecular modeling study of isoindolines as L-type Ca2+ channel blockers by docking calculations

Two series of isoindolines 1(a–g) and 2(a–g) were found by docking calculations to be possible L-type Ca²⁺ channel (LCC) blockers. The theoretical 3-D model of the outer vestibule and the selective filter of the LCC was provided by Professor Lipkind; this model consists of transmembrane segments S5 and S6 and P-loops contributed by each of four repeats (I, II, III, and IV) of Ca_v 1.2. Therefore, two well-known LCC blockers, nifedipine 3 and (R)-ethosuccinimide 4 were also evaluated, and their binding sites on the LCC were identified and compared with those obtained for 1(a–g) and 2(a–g). Analysis of the results shows that the target compounds tested probably could be LCC blockers, since they interact with or near the glutamic acid residues Glu393, Glu736, Glu1145 and Glu1446 (the EEEE locus), which belong to the LCC selectivity region. The ∆G values for all of the Ca²⁺ channel ligands are between−10.78 and −3.67 (kcal mol⁻¹), showing that LCC-1b, -1e and -1f complexes are more stable than the other compounds tested. Therefore, theoretically calculated dissociation constants K _d (μM) were obtained for all compounds. Comparing these values reveals that compounds 1b (0.0244 μM), 1e (0.0176 μM) and 1f (0.0125 μM) exhibit more affinity for the LCC than the other compounds. This screening shows that the two series of isoindolines probably could act as LCC blockers.     

A B3LYP and MP2 theoretical investigation into host-guest interaction between calix[4]arene and Li+ or Na+

The DFT-B3LYP and MP2 methods with 6-311G** and 6-311++G** basis sets have been applied to study the complexation energies of the host-guest complexes between the cone calix[4]arene and Li⁺ or Na⁺ on the B3LYP optimized geometries. A comparison of the complexation energies obtained from the MP2(full) with those from MP2(fc) method is also carried out. The result shows that it is essential to introduce the diffuse basis set into the geometry optimizations and complexation energy calculations of the alkali-metal cation-π interaction complexes of calix[4]arene, and the D _e values show a maximum of 21.13 kJ mol⁻¹ (14.45% of relative error) between the MP2(full)/6-311++G** and MP2(fc)/6-311++G** method. For Li⁺ cation, the complexation is mainly energetically stabilized by the lower rim/cation (namely O–Li⁺) interaction. However, binding energies and NBO analyses confirm that Na⁺ cation prefers to enter the calix[4]arene cavity and the cation-π interaction is predominant, which contradicts the previous low-level theoretical studies. Furthermore, the complexation with Li⁺ is preferred over that with Na⁺ by at least 12.70 kJ mol⁻¹ at MP2(full)/6-311++G**//B3LYP/6-311++G** level.      

Drying of Pomegranate Arils and Selection of a Suitable Drying Model

The drying characteristics of pomegranate arils were investigated in temperature range of 50–70 °C. The increase in drying air temperature resulted in a decrease in drying time. The drying rate was found to increase with temperature, thereby reducing the total drying time. Thirteen drying models were evaluated in the kinetics research. The goodness of fit of the proposed models was evaluated by using the determination of coefficient (R ² ), mean relative percent error (P), reduced chi-square (χ ²), and root means square error (RMSE). The Midilli et al. model showed a better fit to experimental drying data as compared to other models. Effective moisture diffusivity (D _eff) ranged from 9.447 × 10⁻¹¹ to 3.481 × 10⁻¹⁰ m²/s as calculated by the Fick’s second law of diffusion. The temperature dependence of the value of effective moisture diffusivity followed an Arrhenius-type relationship. The activation energy for the moisture diffusion was determined to be 60.34 kJ/mol.     

Production of monoterpenoids and aroma compounds from cell suspension cultures of <Emphasis Type="Italic">Camellia sinensis</Emphasis>

Cell suspension cultures of Camellia sinensis were established in 250 ml shake flasks. Flasks contained 50 ml liquid medium of either Murashige and Skoog (MS), N/5 MS or Heller medium containing different levels of 6-benzyladenine (BA) (0.05–2 mg l⁻¹), 2,4-dichlorophenoxyacetic acid (2,4-D) (1–10 mg l⁻¹), and sucrose (10–50 g l⁻¹). Moreover, the pH of the medium was varied from 5.2–6.2. In addition, cultures were subjected to light irradiation as well as to complete darkness. Following optimization of aroma and terpenoid extraction methods, cell cultures were analyzed for the volatile compounds using GC/MS. A total of 43 compounds were identified using the micro SDE apparatus. Among the major monoterpenoids obtained were α-terpineol and nerol. Moreover, other high aroma-value compounds, including 2-ethyl hexanol, benzyl alcohol, benzene acetaldehyde, nonanal and phenylethylalcohol were also detected. The highest levels of these compounds were obtained from cell suspension cultures grown in MS medium containing 5 mg l⁻¹ 2,4-D, 1 mg l⁻¹ BA and 30 g l⁻¹ sucrose at pH of 5.8 with incubation in complete darkness.     

Toxicity of cadmium and zinc on two microalgae, <Emphasis Type="Italic">Scenedesmus obliquus</Emphasis> and <Emphasis Type="Italic">Desmodesmus pleiomorphus</Emphasis>, from Northern Portugal

Aquatic environments often contain toxic heavy metals that may enter the food web via uptake by microalgae and eventually cause severe poisoning problems at higher trophic levels. The effects of Cd and Zn cations upon growth of two native green microalgal species, Scenedesmus obliquus and Desmodesmus pleiomorphus (previously isolated from a polluted site in Northern Portugal), were accordingly evaluated. Growth inhibition of the microalgal cells was determined following exposure for 96 h to several initial concentrations of aqueous solutions of either of those two metals. At the higher end of Cd and Zn experimental concentration ranges, a significant reduction in cell density was observed in the cultures; EC₅₀ values, calculated after fitting a Weibull model to the experimental data, were 0.058 and 1.92 mg L⁻¹ for Cd and 16.99 and 4.87 mg L⁻¹ for Zn in the case of S. obliquus and D. pleiomorphus, respectively. One observed that S. obliquus can tolerate higher Zn concentrations than D. pleiomorphus, but the reverse holds regarding exposure to Cd.     

Instability of 2,2-di(pyridin-2-yl)acetic acid. Tautomerization versus decarboxylation

The DFT calculations at the B3LYP level with 6-311G** basis set were carried out in order to reveal whether tautomerization or decarboxylation is responsible for the instability of 2,2-di(pyridin-2-yl)acetic (DPA) and 1,8-diazafluorene-9-carboxylic (DAF) acids. The carboxyl protons in both compounds are involved in the intramolecular hydrogen bonds (the pyridine nitrogen atoms are the hydrogen bond acceptors). Although formation of two intramolecular OH···N hydrogen bonds in the enols of both carboxylic acids enables effective electron delocalization within the quasi rings (···HO − C = C − C = N), only ene-1,1-diol of DAF has somewhat lower energy than DAF itself (ΔE is ca. 7 kcal mol^-1). DPA and its enediol have comparable energies. Migration of the methine proton toward the carbonyl oxygen atom (to form enediols) requires overstepping the energy barriers of 55-57 kcal mol^-1 for both DPA and DAF. The enaminone tautomers of the acids, formed by migration of this proton toward the pyridine nitrogen atom, are thermodynamically somewhat more stable than the respective enediols. The energy barriers of these processes are equal to ca. 44 and 62 kcal mol^-1 for DPA and DAF, respectively. Thus, such tautomerization of the acids is not likely to proceed. On the other hand, the distinct energetic effects (ca. 15 kcal mol^-1) favor decarboxylation. This process involves formation of (E)-2-(pyridin-2(1H)-ylidenemethyl)pyridine and its cyclic analogue followed by their tautomerization to (dipyridin-2-yl)methane and 1,8-diazafluorene, respectively. Although the later compound was found to be somewhat thermodynamically more stable, kinetic control of tautomerization of the former is more distinct.     

Formation of Two Different Types of Ion Channels by Amphotericin B in Human Erythrocyte Membranes

The polyene antibiotic amphotericin B (AmB) is known to form aqueous pores in lipid membranes and biological membranes. Here, membrane potential and ion permeability measurements were used to demonstrate that AmB can form two types of selective ion channels in human erythrocytes, differing in their interaction with cholesterol. We show that AmB induced a cation efflux (negative membrane polarization) across cholesterol-containing liposomes and erythrocytes at low concentrations (≤1.0 × 10⁻⁶ M), but a sharp reversal of such polarization was observed at concentrations greater than 1.0 × 10⁻⁶ M AmB, an indication that aqueous pores are formed. Cation-selective AmB channels are also formed across sterol-free liposomes, but aqueous pores are only formed at AmB concentrations 10 times greater. The effect of temperature on the AmB-mediated K⁺ efflux across erythrocytes revealed that the energies of activation for channel formation are negative and positive at AmB concentrations that lead predominantly to the formation of cation-selective channels and aqueous pores, respectively. These findings support the conclusion that the two types of AmB channels formed in human erythrocytes differ in their interactions with cholesterol and other membrane components. In effect, a membrane lipid reorganization, as induced by incubation of erythrocytes with tetrathionate, a cross-linking agent of the lipid raft–associated protein spectrin, led to differential changes in the activation parameters for the formation of both types of channels, reflecting the different lipid environments in which such structures are formed.     

Arsenic accumulation and thiol status in lichens exposed to As(V) in controlled conditions

Thalli of epiphytic lichen Hypogymnia physodes (L.) Nyl. and terricolous Cladonia furcata (Huds.) Schrad., collected from an area with background arsenic concentrations, were exposed to 0, 0.1, 1 and 10 μg mL⁻¹ arsenate (As(V)) solutions for 24 h. After exposure they were kept in the metabolically active state for 0, 24 and 48 h in a growth chamber. In the freeze dried samples glutathione (GSH), glutathione disulphide (GSSG), cysteine (Cys) and cystine were analysed and induction of phytochelatin (PC) synthesis measured by reversed-phase high-performance liquid chromatography in combination with fluorescence detection or UV spectrometry. Total arsenic content in thalli was measured by instrumental neutron activation analysis (INAA). In H. physodes, which contained higher amounts of arsenic compared to C. furcata, total glutathione content significantly decreased in samples exposed to 10 μg mL⁻¹ As(V), whereas in C. furcata a significant increase was observed. In both species PC synthesis was induced in thalli exposed to 10 μg mL⁻¹.     

Conformational stabilities, infrared, and vibrational dichroism spectroscopy studies of tris(ethylenediamine) zinc(II) chloride

The conformational stabilities of the transition metal complex of Zn (en)₃Cl₂ were studied using density functional theory (DFT). Deformational potential energy profiles (PEPs), and pathways between the different isomeric conformational energies were calculated using DFT/B3LYP/6–31G. The relative conformational energies of Δ(λλλ), Δ(λλδ), Δ(λδδ) and Δ(δδδ) are 10.48, 7.08, 3.56, and 0.0 kcal/mol, respectively, which are small compared to the barrier heights for reversible phase transitions (49.56, 49.55, 49.52 kcal/mol, respectively). Frequency assignment was carried out by decomposing Fourier transform infrared (FTIR) spectra using Gaussian and Gaussview. The theoretical IR and vibrational dichroism spectroscopy (VCD) absorption spectra are presented for all conformations within the range of 400–3,500 cm^-1.     

Developing novel approaches to improve binding energy estimation and virtual screening: a PARP case study

Poly-(ADP-ribose)-polymerase (PARP) is a promising anti-cancer target as it plays a crucial role in the cellular reparation and survival mechanisms. However, the development of a robust and cost effective experimental technique to screen PARP inhibitors is still a scientific challenge owing to the difficulties in quantitative detection of the enzyme activity. In this work we demonstrate that the computational chemistry tools including molecular docking and scoring can perform on par with the experimental studies in assessing binding constants and in the recovery of active compounds in virtual screening. Using the recently introduced Lead Finder software we were able to dock a set of 142 well characterized PARP inhibitors and obtain a good correlation between the calculated and experimentally measured binding energies with the rmsd of 1.67 kcal mol⁻¹. Additionally, fine-tuning of the energy scaling coefficients within the Lead Finder scoring function has further decreased rmsd to the value of 0.88 kcal mol⁻¹. Moreover, we were able to reproduce the selectivity of ligand binding between the two isoforms of the enzyme-PARP1 and PARP2-suggesting that the Lead Finder software can be used to design isoform-selective inhibitors of PARP. An impressive enrichment was obtained in the virtual screening experiment, in which the mentioned set of PARP inhibitors was mixed with a commercial library of 300,000 compounds. We also demonstrate that the virtual screening performance can be significantly improved by an additional structural filtration of the docked ligand poses through detection of the crucial hydrogen bonding interactions with the enzyme.     

Optimization of fermentation medium for triterpenoid production from <Emphasis Type="Italic">Antrodia camphorata</Emphasis> ATCC 200183 using artificial intelligence-based techniques

In this study, alteration in morphology of submergedly cultured Antrodia camphorata ATCC 200183 including arthroconidia, mycelia, external and internal structures of pellets was investigated. Two optimization models namely response surface methodology (RSM) and artificial neural network (ANN) were built to optimize the inoculum size and medium components for intracellular triterpenoid production from A. camphorata. Root mean squares error, R ², and standard error of prediction given by ANN model were 0.31%, 0.99%, and 0.63%, respectively, while RSM model gave 1.02%, 0.98%, and 2.08%, which indicated that fitness and prediction accuracy of ANN model was higher when compared to RSM model. Furthermore, using genetic algorithm (GA), the input space of ANN model was optimized, and maximum triterpenoid production of 62.84 mg l⁻¹ was obtained at the GA-optimized concentrations of arthroconidia (1.78 × 10⁵ ml⁻¹) and medium components (glucose, 25.25 g l⁻¹; peptone, 4.48 g l⁻¹; and soybean flour, 2.74 g l⁻¹). The triterpenoid production experimentally obtained using the ANN–GA designed medium was 64.79 ± 2.32 mg l⁻¹ which was in agreement with the predicted value. The same optimization process may be used to optimize many environmental and genetic factors such as temperature and agitation that can also affect the triterpenoid production from A. camphorata and to improve the production of bioactive metabolites from potent medicinal fungi by changing the fermentation parameters.     

Analysis of a continuous culture of Fibrobacter succinogenes S85 on a standardized glucose medium

Continuous cultures of Fibrobacter succinogenes S85 were performed on a standardized fully synthetic culture medium with glucose as carbon source at a dilution rate (D = 0.02 h⁻¹) in a 5-L bioreactor. The culture was stabilized during 20 days and demonstrated the ability of Fibrobacter succinogenes to grow in this synthetic medium. CO₂ partial pressure and redox potential probes were used to check the anaerobic state of the culture. The biomass yield was calculated 0.206 g (g glucose)⁻¹ and the production yield of succinate, the major end-product, was 0.63 mol (mol glucose)⁻¹. The consistency of the experimental data was checked by proton and mass (C, N) balances. The results were satisfactory (90–110% recovery) leading to derive a stoichiometric equation representative of the growth on glucose. The stoichiometric coefficients were calculated using data reconciliation and linear algebra methods enabling to obtain a complete modeling of all conversion yields possible.