A Rapid Method for the Determination of Fucoxanthin in Diatom.

Fucoxanthin is a natural pigment found in microalgae, especially diatoms and Chrysophyta. Recently, it has been shown to have anti-inflammatory, anti-tumor, and anti-obesityactivity in humans. Phaeodactylum tricornutum is a diatom with high economic potential due to its high content of fucoxanthin and eicosapentaenoic acid. In order to improve fucoxanthin production, physical and chemical mutagenesis could be applied to generate mutants. An accurate and rapid method to assess the fucoxanthin content is a prerequisite for a high-throughput screen of mutants. In this work, the content of fucoxanthin in P. tricornutum was determined using spectrophotometry instead of high performance liquid chromatography (HPLC). This spectrophotometric method is easier and faster than liquid chromatography and the standard error was less than 5% when compared to the HPLC results. Also, this method can be applied to other diatoms, with standard errors of 3-14.6%. It provides a high throughput screening method for microalgae strains producing fucoxanthin.

State-resolved differential and integral cross sections for the Ne + H2 (+) (v = 0-2, j = 0) → NeH(+) + H reaction.

State-to-state quantum dynamic calculations for the proton transfer reaction Ne + H2 (+) (v = 0-2, j = 0) are performed on the most accurate LZHH potential energy surface, with the product Jacobi coordinate based time-dependent wave packet method including the Coriolis coupling. The J = 0 reaction probabilities for the title reaction agree well with previous results in a wide range of collision energy of 0.2-1.2 eV. Total integral cross sections are in reasonable agreement with the available experiment data. Vibrational excitation of the reactant is much more efficient in enhancing the reaction cross sections than translational and rotational excitation. Total differential cross sections are found to be forward-backward peaked with strong oscillations, which is the indication of the complex-forming mechanism. As the collision energy increases, state-resolved differential cross section changes from forward-backward symmetric peaked to forward scattering biased. This forward bias can be attributed to the larger J partial waves, which makes the reaction like an abstraction process. Differential cross sections summed over two different sets of J partial waves for the v = 0 reaction at the collision energy of 1.2 eV are plotted to illustrate the importance of large J partial waves in the forward bias of the differential cross sections.

Reactant coordinate based state-to-state reactive scattering dynamics implemented on graphical processing units.

A parallel code for state-to-state quantum dynamics with propagation of time-dependent wavepacket in reactant coordinates has been developed on graphical processing units (GPUs). The propagation of wavepacket and the transformation of wavepacket from reactant to product Jacobi coordinates are entirely calculated on GPUs. A new interpolation procedure is introduced for coordinate transformation to decrease the five-loop computation to two four-loop computations. This procedure has a negligible consumption of extra GPU memory in comparison with that of the wavepacket and produces a considerable acceleration of the computational speed of the transformation. The code is tested to get differential cross sections of H+HD reaction and state-resolved reaction probabilities of O+HD for total angular momenta J = 0, 10, 20, and 30. The average speedups are 57.0 and 83.5 for the parallel computations on two C2070 and K20m GPUs relative to serial computation on Intel E5620 CPU, respectively.

Time-dependent wave-packet quantum dynamics study of the Ne + D2(+) (v0 = 0-2, j0 = 0) → NeD(+) + D reaction: including the coriolis coupling.

The dynamics of the Ne + D2(+) (v0 = 0-2, j0 = 0) → NeD(+) + D reaction has been investigated in detail by using an accurate time-dependent wave-packet method on the ground 1(2)A' potential energy surface. Comparisons between the Coriolis coupling results and the centrifugal-sudden ones reveal that Coriolis coupling effect can influence reaction dynamics of the NeD2(+) system. Integral cross sections have been evaluated for the Ne + D2(+) reaction and its isotopic variant Ne + H2(+), and a considerable intermolecular isotopic effect has been found. Also obvious is the great enhancement of the reactivity due to the reagent vibrational excitation. Besides, a comparison with previous theoretical results is also presented and discussed.

Adiabatic/nonadiabatic state-to-state reactive scattering dynamics implemented on graphics processing units.

An efficient graphics processing units (GPUs) version of time-dependent wavepacket code is developed for the atom-diatom state-to-state reactive scattering processes. The propagation of the wavepacket is entirely calculated on GPUs employing the split-operator method after preparation of the initial wavepacket on the central processing unit (CPU). An additional split-operator method is introduced in the rotational part of the Hamiltonian to decrease communication of GPUs without losing accuracy of state-to-state information. The code is tested to calculate the differential cross sections of H + H2 reaction and state-resolved reaction probabilities of nonadiabatic triplet-singlet transitions of O((3)P,(1)D) + H2 for the total angular momentum J = 0. The global speedups of 22.11, 38.80, and 44.80 are found comparing the parallel computation of one GPU, two GPUs by exact rotational operator, and two GPU versions by an approximate rotational operator with serial computation of the CPU, respectively.

Nonadiabatic ab initio molecular dynamics of photoisomerization in bridged azobenzene.

The photoisomerization mechanisms of bridged azobenzene are investigated by means of surface hopping dynamics simulations based on the Zhu-Nakamura theory. In the geometry optimizations and potential energy surface calculations, four minimum-energy conical intersections between the ground state and the lowest excited state are found to play important roles in the trans-cis and cis-trans isomerization processes. The trans-cis photoisomerization proceeds through two minimum-energy conical intersections. Ultrafast pedal motion of the N atoms and twisting of phenyl rings around their N-C bonds allows the molecule to move to a minimum-energy conical intersection, after which surface hopping from S(1) to S(0) occurs. In the S(0) state, further rotation occurs around the N=N bond and two N-C bonds until the azo moiety and phenyl rings complete their isomerization. Finally, the cis form is achieved by subsequent adjustment of the ethylene bridge. In the cis-trans photodynamics, there is one rotational pathway, in the middle of which two CIs are responsible for the surface hopping to the S(0) state. After the nonadiabatic transition, the molecule reaches the trans form through a barrierless pathway and the two phenyl rings and the additional bridge complete their reorientation almost at the same time.

Dissociation and ionization competing processes for H2+ in intense laser field: which one is larger?

Competition between dissociation and ionization of H(2)(+) in intense laser field has been investigated by using an accurate three-dimensional time-dependent wavepacket approach. The disagreement between the experiment and the former one-dimensional theory has been resolved. In a comparison of the calculated results with the available experimental data, a good agreement is reached, not only for the relative probabilities between dissociation and ionization but also for the two-peak structures and the peak energy locations for these two processes.

Exact quantum scattering study of the H + HS reaction on a new ab initio potential energy surface H2S (3A").

We present an exact quantum dynamical study and quasi-classical trajectory (QCT) calculations for the exchange and abstraction processes for the H + HS reaction. These calculations were based on a newly constructed high-quality potential energy surface for the lowest triplet state of H(2)S ((3)A"). The ab initio single-point energies were computed using complete active space self-consistent field and multi-reference configuration interaction method with a basis set of aug-cc-pV5Z. The time-dependent wave packet (TDWP) method was used to calculate the total reaction probabilities and integral cross sections over the collision energy (E(col)) range of 0.0-2.0 eV for the reactant HS initially at the ground state and the first vibrationally excited state. It was found that the initial vibrational excitation of HS enhances both abstraction and exchange processes. In addition, a good agreement is found between QCT and TDWP reaction probabilities at the total momentum J = 0 as a function of collision energy for the H + HS (v = 0, j = 0) reaction.

Quantum dynamical study of the electronic nonadiabaticity in the D + DBr → Br(Br*) + D2 reaction on new diabatic potential energy surfaces.

A set of diabatic potential energy surfaces, that describe the D + DBr → Br(P(1/2,3/2)) + D(2) reaction, is constructed based on MRCI/aug-cc-pV5Z calculations at 29,526 grid points. Time-dependent wave packet calculations are performed for ground-state DBr initially with collision energies up to 2.0 eV to investigate possible electronic nonadiabaticity in this reaction. Reaction probabilities and integral cross sections are calculated. The results show negligible nonadiabatic effects for the title reaction in the energy range considered here, confirming experimental work of Zare and co-workers. In addition, the calculated thermal rate constants are in good agreement with experimental ones.

Quenching of OH(A(2)Sigma(+)) by H(2) through conical intersections: highly excited products in nonreactive channel.

Nonadiabatic quantum scattering calculations have been carried out for the reactive and nonreactive quenching of OH(A(2)Sigma(+)) in collisions with molecular H(2) on two new potential energy surfaces of the 1A' and 2A' states. Integral cross sections of the reactive and nonreactive quenching channels and the quantum state distributions of the nonreactive channel have been obtained. The theory reveals a high degree of rotational excitation of the quenched OH(X(2)II) products and vibrational excitation of the H(2) products. The calculated results are in good agreement with the existing experimental data. The topography of the potential energy surfaces in the conical intersection regions is provided in order to discuss the origin of the internal excitations of nonreactive products and the branching of the reactive and nonreactive channels.

Exact quantum scattering study of the Ne+H(2) (+) reaction on a new ab initio potential energy surface.

We present a new potential energy surface (PES) for the ground state (1(2)A(')) of the chemical reaction Ne+H(2) (+) from a set of accurate ab initio data, which were computed using highly correlated complete active space self-consistent field and multireference configuration interaction wave functions with a basis set of aug-cc-pV5Z. The quantum reactive scattering dynamics calculation was carried out over the collision energy (E(col)) range of 0.5-1.5 eV based on the new PES. In this work we have taken the Coriolis coupling (CC) effect into account. The importance of including the CC quantum scattering calculation has been revealed by the comparison between the CC and the centrifugal sudden approximation calculation. The magnitude and profile of the CC total cross sections for v=0 and j=1 over the collision energy range of 0.5-1.5 eV are found to be in good agreement with the available experimental measurements obtained recently by Zhang et al. [J. Chem. Phys. 119, 10175 (2003)] after taking into account the experimental uncertainties.

Nonadiabatic quantum reactive scattering of the OH(A 2Σ+) + D2.

The seams of conical intersection exist between the ground (1 (2)A(')) and the first-excited (2 (2)A(')) electronic potential energy surfaces (PESs) of OH(A (2)Σ(+),X (2)Π) + H(2) system. This intersection induces the nonadiabatic quenching of OH(A (2)Σ(+)) by D(2). We present nonadiabatic quantum dynamics study for OH(A (2)Σ(+)) + D(2) on new five-dimensional coplanar PESs. The ab initio calculations of PESs are based on multireference configuration interaction (MRCI)/aug-cc-pVQZ level. A back-propagation neural network is utilized to fit the PESs and nonadiabatic coupling. High degrees of rotational excitation of quenched OH(X (2)Π) products are found in nonreactive quenching channel, and the quenched D(2) products are vibrationally excited up to quantum number v(2) (')=8. The theoretical results of nonadiabatic time-dependent wave-packet calculation are in good agreement with the existing experimental data.

A fluorophore's electron-deficiency does matter in designing high-performance near-infrared fluorescent probes.

The applications of most fluorescent probes available for Glutathione S-Transferases (GSTs), including NI3 which we developed recently based on 1,8-naphthalimide (NI), are limited by their short emission wavelengths due to insufficient penetration. To realize imaging at a deeper depth, near-infrared (NIR) fluorescent probes are required. Here we report for the first time the designing of NIR fluorescent probes for GSTs by employing the NIR fluorophore HCy which possesses a higher brightness, hydrophilicity and electron-deficiency relative to NI. Intriguingly, with the same receptor unit, the HCy-based probe is always more reactive towards glutathione than the NI-based one, regardless of the specific chemical structure of the receptor unit. This was proved to result from the higher electron-deficiency of HCy instead of its higher hydrophilicity based on a comprehensive analysis. Further, with caging of the autofluorescence being crucial and more difficult to achieve via photoinduced electron transfer (PET) for a NIR probe, the quenching mechanism of HCy-based probes was proved to be PET for the first time with femtosecond transient absorption and theoretical calculations. Thus, HCy2 and HCy9, which employ receptor units less reactive than the one adopted in NI3, turned out to be the most appropriate NIR probes with high-sensitivity and little nonenzymatic background noise. They were then successfully applied to detecting GST in cells, tissues and tumor xenografts in vivo. Additionally, unlike HCy2 with a broad isoenzyme selectivity, HCy9 is specific for GSTA1-1, which is attributed to its lower reactivity and the higher effectiveness of GSTA1-1 in stabilizing the active intermediate via H-bonds based on docking simulations.

Inhibition of Rat CYP1A2 and CYP2C11 by Honokiol, a Component of Traditional Chinese Medicine.

BACKGROUND AND OBJECTIVES: Honokiol, a major constituent isolated from Magnolia officinalis, is regarded as a phytochemical marker and bioactive substance present in many traditional Chinese medicines. However, the effect of honokiol on cytochrome P450 (CYP) has not been thoroughly investigated. The aim of this study was to investigate the effect of honokiol on CYP1A2 and CYP2C11 in vitro and in vivo. METHODS: The effect of honokiol on CYP1A2 and CYP2C11 was investigated with rat liver microsomes (RLMs) by measuring phenacetin and tolbutamide metabolism (probe drugs for CYP1A2 and CYP2C11, respectively), and then explored in vivo by measuring the effect of honokiol (2.5 and 5 mg/kg, intravenous injection) on the pharmacokinetics of theophylline and tolbutamide (probe drugs for CYP1A2 and CYP2C11, respectively) in rats in vivo. RESULTS: Honokiol inhibited the formation of acetaminophen from phenacetin and 4-hydroxytolbutamide from tolbutamide in RLMs, with inhibition constant (Ki) values of 1.6 µM and 16.5 µM, respectively. In vivo, honokiol (2.5 or 5.0 mg/kg) increased the half-life (t1/2) of theophylline by 40.9% and 119.9%, decreased the clearance (CL) by 23.8% and 42.9%, and increased the area under the curve (AUC) by 41.3% and 83.4%, respectively. Similarly, the t1/2 of tolbutamide increased by 25.5% and 33.8%, the CL decreased by 14.3% and 19.1%, and the AUC increased by 19.2% and 25.7%, respectively. CONCLUSION: The inhibition of CYP1A2 by honokiol is greater than the inhibition of CYP2C11. The changes in the pharmacokinetics of theophylline and tolbutamide in rats treated with honokiol are due to the inhibition of CYP1A2 and CYP2C11 activity in a dose-dependent manner.

[Rapid Cultivation of Anaerobic Ammonium Oxidation Granular Sludge and Inhibition Kinetics of Granular Sludge].

For the rapid cultivation of anaerobic ammonium oxidation (ANAMMOX) granular sludge (AGS), a small amount of flocculent ANAMMOX sludge (FAS) was taken as the research object, and a bio-flow separate ball was used as the filler in an up-flow anaerobic sludge bed (UASB) to rapidly begin ANAMMOX and to cultivate granular sludge. In addition, the substrate inhibition kinetic characteristics of the AGS were investigated by using the Haldane model. The results showed that start-up of the ANAMMOX was successfully achieved. The total nitrogen removal rate was more than 85%, and the volume load of total nitrogen was 0.72 kg·(m3·d)-1. AGS with diameters of 1.0-3.0 mm were cultured within 127 days using the Bio-flow Separate Ball. The kinetic studies showed that the maximum reaction rates for ammonia and nitrite of granular sludge were 1.46 kg·(kg·d)-1 and 1.76 kg·(kg·d)-1, with half inhibition constants of ammonia and nitrite at 852.2 mmol·L-1 and 108.2 mmol·L-1, respectively. Compared with FAS, AGS can withstand higher concentrations of ammonia and nitrite and can maintain a higher reaction rate. The placement of the filler has positive significance for starting ANAMMOX and rapidly culturing AGS.

Attosecond-resolution quantum dynamics calculations for atoms and molecules in strong laser fields.

A parallel quantum electron and nuclei wave packet computer code, LZH-DICP, has been developed to study laser-atom-molecule interaction in the nonperturbative regime with attosecond resolution. The nonlinear phenomena occurring in that regime can be studied with the code in a rigorous way by numerically solving the time-dependent Schrödinger equation of electrons and nuclei. Time propagation of the wave functions is performed using a split-operator approach, and based on a sine discrete variable representation. Photoelectron spectra for hydrogen and kinetic-energy spectra for molecular hydrogen ion in linearly polarized laser fields are calculated using a flux operator scheme, which testifies to the validity and the high efficiency of LZH-DICP.

Tuning peptide self-assembly by an in-tether chiral center.

The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical peptides with high controllability and tunability is challenging. We report a new self-assembling mode that uses in-tether chiral center-induced helical peptides as a platform for tunable peptide self-assembly with good controllability. It was found that self-assembling behavior was governed by in-tether substitutional groups, where chirality determined the formation of helical structures and aromaticity provided the driving force for self-assembly. Both factors were essential for peptide self-assembly to occur. Experiments and theoretical calculations indicate long-range crystal-like packing in the self-assembly, which was stabilized by a synergy of interpeptide π-π and π-sulfur interactions and hydrogen bond networks. In addition, the self-assembled peptide nanomaterials were demonstrated to be promising candidate materials for applications in biocompatible electrochemical supercapacitors.

[Isolation, Identification and Nitrogen Removal Characteristics of a Heterotrophic Nitrification-Aerobic Denitrification Strain y3 Isolated from Marine Environment].

A heterotrophic nitrification--aerobic denitrification bacterium named y3 was isolated from the sludge of Jiaozhou Bay using the enrichment medium with seawater as the matrix. It was identified as Pseudomonas sp. based on the morphological observation, physiological experiments and sequence analysis of 16S rRNA. The experiment results showed that the optimal carbon resource was sodium citrate, the optimal pH was 7.0, and the optimal C/N was 13. The strain could use NH4Cl, NaNO2 and KNO3 as sole nitrogen source, and the removal efficiencies were 98.69%, 78.38% and 72.95% within 20 hours, respectively. There was no nitrate and nitrite accumulation during the heterotrophic nitrification process. Within 20 hours, the nitrogen removal efficiencies were 99.56%, 99.75% and 99.41%, respectively, in the mixed system with NO3⁻-N: NO²â»-N of 2:1, 1:1 and 1:2. When the NH4⁺-N: NO3⁻-N ratios were 2: 1 , 1: 1 , 1: 2, the nitrogen removal efficiencies were all 100% . When the NH4⁺-N:NO2⁻-N ratios were 2:1,1:1,1:2, the nitrogen removal efficiencies were 90.43%, 92.79% and 99.96%, respectively. They were higher than those with single nitrogen source. As a result, strain y3 had good nitrogen removal performance in high saline wastewater treatment.

Synergistic Cellulose Hydrolysis Dominated by a Multi-Modular Processive Endoglucanase from Clostridium cellulosi.

Recalcitrance of biomass feedstock remains a challenge for microbial conversion of lignocellulose into biofuel and biochemicals. Clostridium cellulosi, one thermophilic bacterial strain dominated in compost, could hydrolyze lignocellulose at elevated temperature by secreting more than 38 glycoside hydrolases belong to 15 different families. Though one multi-modular endoglucanase CcCel9A has been identified from C. cellulosi CS-4-4, mechanism of synergistic degradation of cellulose by various cellulases from strain CS-4-4 remains elusive. In this study, CcCel9A, CcCel9B, and CcCel48A were characterized as processive endoglucanase, non-processive endoglucanase, and exoglucanase, respectively. To understand how they cooperate with each other, we estimated the approximate concentration ratio on the zymogram and optimized it using purified enzymes in vitro. Synergism between individual glycoside hydrolase during cellulose hydrolysis in the mixture was observed. CcCel9A and CcCel48A could degrade cellulose chain from non-reducing ends and reducing ends, respectively, to cello-oligosaccharide. CcCel9B could cut cellulose chain randomly and cello-oligosaccharides with varied length were released. In addition, a ß-glucosidase BlgA from Caldicellulosiruptor sp. F32 which could cleave cello-oligosaccharides including G2-G6 to glucose was added to the enzyme mixture to remove the product inhibition of its partners. The combination and ratios of these cellulases were optimized based on the release rate of glucose. Hydrolysis of corn stalk was conducted by a four-component cocktail (CcCel9A:CcCel9B:CcCel48A:BlgA = 25:25:10:18), and only glucose was detected as main production by using high-performance anion-exchange chromatography. Processive endoglucanase CcCel9A, dominated in secretome of C. cellulosi, showed good potential in developing cellulase cocktail due to its exquisite cooperation with various cellulases.

[Identification and Nitrogen Removal Characteristics of a Heterotrophic Nitrification-Aerobic Denitrification Strain Isolated from Marine Environment].

A heterotrophic nitrification-aerobic denitrification strain named y5 was isolated from marine environment by traditional microbial isolation method using seawater as medium. It was identified as Klebsiella sp. based on the morphological, physiological and 16S rRNA sequence analysis. The experiment results showed that the optimal carbon resource was sodium citrate; the optimal pH was 7.0; and the optimal C/N was 17. The strain could use NH4Cl, NaNO2 and KNO3 as sole nitrogen source, and the removal efficiencies were77.07%, 64.14% and 100% after 36 hours, respectively. The removal efficiency reached 100% after 36 hours in the coexistence of NH4Cl, NaNO2 and KNO3. The results showed that the strain y5 had independent and efficient heterotrophic nitrification and aerobic denitrification activities in high salt wastewater.