Comprehensive analysis of the effect of rs2295080 and rs2536 polymorphisms within the mTOR gene on cancer risk.

There is still no conclusion on the potential effect of the rs2295080 and rs2536 polymorphisms of mTOR (mammalian target of rapamycin) gene on different cancers. Herein, we performed a comprehensive assessment using pooled analysis, FPRP (false-positive report probability), TSA (trial sequential analysis), and eQTL (expression quantitative trait loci) analysis. Eighteen high-quality articles from China were enrolled. The pooled analysis of rs2295080 with 9502 cases and 10,965 controls showed a decreased risk of urinary system tumors and specific prostate cancers [TG vs. TT, TG+GG vs. TT and G vs. T; P<0.05, OR (odds ratio) <1]. FPRP and TSA data further confirmed these results. There was an increased risk of leukemia [G vs. T, GG vs. TT, and GG vs. TT+TG genotypes; P<0.05, OR>1]. The eQTL data showed a potential correlation between the rs2295080 and mTOR expression in whole blood samples. Nevertheless, FPRP and TSA data suggested that more evidence is required to confirm the potential role of rs2295080 in leukemia risk. The pooled analysis of rs2536 (6653 cases and 7025 controls) showed a significant association in the subgroup of "population-based" control source via the allele, heterozygote, dominant, and carrier comparisons (P<0.05, OR>1). In conclusion, the TG genotype of mTOR rs2295080 may be linked to reduced susceptibility to urinary system tumors or specific prostate cancers in Chinese patients. The currently data do not strongly support a role of rs2295080 in leukemia susceptibility. Large sample sizes are needed to confirm the potential role of rs2536 in more types of cancer.

Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model.

Based on an electrochemical multiphysical simulation, a method for analysing electrolysis efficiency has been presented that considers the energy consumption required to produce a single kilogram of lithium and for the production of lithium, rather than the voltage in various parts. By adopting them as the criteria for analysing electrolysis efficiency in the lithium cell, several structural parameters have been optimized, such as the anode radius and anode-cathode distance. These parameters strongly affect the cell voltage and the velocity field distribution, which has a significant impact on the concentration distribution. By integrating the concentration distribution, the lithium production and energy consumption per kilogram, lithium is computed. By appointing the minimum of the chlorine and lithium concentration as the secondary reaction intensity, it is clear where the secondary reaction intensity is strong in the cell. The structure of a lithium electrolysis cell has been optimized by applying an orthogonal design approach, with the energy consumption notably decreasing from 35.0 to 28.3 kWh (kg Li)-1 and the lithium production successfully increasing by 0.17 mol.

Computational fluid dynamics simulation as a tool for optimizing the hydrodynamic performance of membrane bioreactors.

The hydrodynamic properties and shear stresses experienced by a membrane bioreactor (MBR) are directly related to its rate of membrane fouling. In this study, computational fluid dynamic models have been combined with cold model PIV experimental studies to optimize the performance properties of MBRs. The effects of membrane module height, number of aeration tubes and membrane spacing on liquid phase flow rates, gas holdup and shear stresses at the membrane surface have been investigated. It has been found that optimal MBRs experience the greatest shear forces on their surfaces at a distance of 250 mm from the aeration tube, around the 7 aeration tubes used to introduce gas and at the 40 mm spacings between the membrane sheets. Use of an aeration intensity of between 0.02 and 0.47 m3 min-1 generated shear stresses that were 50-85% higher than the original MBR for the same aeration intensity, thus affording optimal membrane performance that minimizes membrane fouling.

Hydrodynamic characteristics of the two-phase flow field at gas-evolving electrodes: numerical and experimental studies.

Gas-evolving vertical electrode system is a typical electrochemical industrial reactor. Gas bubbles are released from the surfaces of the anode and affect the electrolyte flow pattern and even the cell performance. In the current work, the hydrodynamics induced by the air bubbles in a cold model was experimentally and numerically investigated. Particle image velocimetry and volumetric three-component velocimetry techniques were applied to experimentally visualize the hydrodynamics characteristics and flow fields in a two-dimensional (2D) plane and a three-dimensional (3D) space, respectively. Measurements were performed at different gas rates. Furthermore, the corresponding mathematical model was developed under identical conditions for the qualitative and quantitative analyses. The experimental measurements were compared with the numerical results based on the mathematical model. The study of the time-averaged flow field, three velocity components, instantaneous velocity and turbulent intensity indicate that the numerical model qualitatively reproduces liquid motion. The 3D model predictions capture the flow behaviour more accurately than the 2D model in this study.

Coupled electro-thermal field in a high current electrolysis cell or liquid metal batteries.

Coupled electro-thermal field exists widely in chemical batteries and electrolysis industry. In this study, a three-dimensional numerical model, which is based on the finite-element software ANSYS, has been built to simulate the electro-thermal field in a magnesium electrolysis cell. The adjustment of the relative position of the anode and cathode can change the energy consumption of the magnesium electrolysis process significantly. Besides, the current intensity has a nonlinear effect on heat balance, and the effects of heat transfer coefficients, electrolysis and air temperature on the heat balance have been released to maintain the thermal stability in a magnesium electrolysis cell. The relationship between structure as well as process parameters and electro-thermal field has been obtained and the simulation results can provide experience for the scale-up design in liquid metal batteries.

Leaching process for recovering valuable metals from the LiNi1/3Co1/3Mn1/3O2 cathode of lithium-ion batteries.

In view of the importance of environmental protection and resource recovery, recycling of spent lithium-ion batteries (LIBs) and electrode scraps generated during manufacturing processes is quite necessary. An environmentally sound leaching process for the recovery of Li, Ni, Co, and Mn from spent LiNi1/3Co1/3Mn1/3O2-based LIBs and cathode scraps was investigated in this study. Eh-pH diagrams were used to determine suitable leaching conditions. Operating variables affecting the leaching efficiencies for Li, Ni, Co, and Mn from LiNi1/3Co1/3Mn1/3O2, such as the H2SO4 concentration, temperature, H2O2 concentration, stirring speed, and pulp density, were investigated to determine the most efficient conditions for leaching. The leaching efficiencies for Li, Ni, Co, and Mn reached 99.7% under the optimized conditions of 1M H2SO4, 1vol% H2O2, 400rpm stirring speed, 40g/L pulp density, and 60min leaching time at 40°C. The leaching kinetics of LiNi1/3Co1/3Mn1/3O2 were found to be significantly faster than those of LiCoO2. Based on the variation in the weight fraction of the metal in the residue, the "cubic rate law" was revised as follows: θ(1-f)1/3=(1-kt/r0ρ), which could characterize the leaching kinetics optimally. The activation energies were determined to be 64.98, 65.16, 66.12, and 66.04kJ/mol for Li, Ni, Co, and Mn, respectively, indicating that the leaching process was controlled by the rate of surface chemical reactions. Finally, a simple process was proposed for the recovery of valuable metals from spent LiNi1/3Co1/3Mn1/3O2-based LIBs and cathode scraps.

Recovery of cathode materials and Al from spent lithium-ion batteries by ultrasonic cleaning.

Cathode materials are difficult to separate from Al-foil substrates during the recycling of spent lithium-ion batteries (LIBs), because of the strong bonding force present. In this study, ultrasonic cleaning was used to separate and recycle these cathode materials. The mechanism of separation was ascribed to the dissolution of polyvinylidene fluoride (PVDF) and the cavitation caused by ultrasound. Based on this mechanism, the key parameters affecting the peel-off efficiency of cathode materials from Al foil was identified as solvent nature, temperature, ultrasonic power, and ultrasonic time. The peel-off efficiency of cathode materials achieved ∼ 99% under the optimized conditions of N-methyl-2-pyrrolidone (NMP) cleaning fluid, 70°C process temperature, 240 W ultrasonic power, and 90 min of ultrasonication. The cathode materials separated from Al foil displayed a low agglomeration degree, which is beneficial to the subsequent leaching process. Finally, a new, environmentally-sound process was proposed to efficiently recycle cathode materials and Al from spent LIBs, consisting of manual dismantling, ultrasonic cleaning, and picking.

[Response Mechanism of Trace Metals in the Bishuiyan Subterranean River to the Rainfall and Their Source Analysis].

High-frequency sampling was conducted at the outlet of Guangxi Bishuiyan karst subterranean river using an automatic sampler during the rainfall events. The hydrochemical drymanic variation characteristics of trace metals (Cu, Pb, Zn, Cd) at the outlet of Guangxi Bishuiyan karst subterranean river were analyzed, and the sources of the trace metals in the subterranean river as well as their response to rainfall were explored. The results showed that the rainfall provoked a sharp decrease in the major elements (Ca²âº, Mg²âº, HCO3⁻, etc.) due to dilution and precipitation, while it also caused an increase in the concentrations of dissolved metals including Al, Mn, Cu, Zn and Cd, due to water-rock reaction, sediment remobilization, and soil erosion. The water-rock reaction was more sensitive to rainfall than the others, while the sediment remobilization and soil erosion took the main responsibility for the chemical change of the heavy metals. The curves of the heavy metal concentrations presented multiple peaks, of which the maximum was reached at 9 hours later after the largest precipitation. Different metal sources and the double-inlet structure of the subterranean river were supposed to be the reasons for the formation of multiple peaks. During the monitoring period, the average speed of the solute in the river reached about 0.47 km · h⁻¹, indicating fast migration of the pollutants. Therefore, monitoring the chemical dynamics of the karst subterranean river, mastering the sources and migration characteristics of trace metal components have great significance for the subterranean river environment pollution treatment.

[Effects of P and K fertilizer on content of coumarin and yield of Glehnia littoralis].

By a orthogonal experiment, the influence of different ratio of phosphorus and potassium fertilizers on imperatorin, isoimperatorin and psoralen contents and yield of Glehnia littoralis were studied. The results showed that root dry weight and the yield of G. littoralis increased when reasonably applied phosphorus fertilizer combined with potassium fertilizer within a certain range. And the influence of phosphorus fertilizer was greater than that of potassium fertilizer. The optimal value of root dry weight and yield achieved at both P2O5 360 kg x hm(-2), K2O 270 kg x hm(-2) and P2O5 360 kg x hm(-2), K2O 180 kg x hm(-2). The effects of different phosphorus and potassium treatments on the content of imperatorin, isoimperatorin and psoralen in G. littoralis were determined, which shows that the content increased with the moderate increase of phosphorus and potassium. And the effects of phosphorus fertilizer were more significantly. The isoimperatorin content achieved the largest value at P2O5 360 kg x hm(-2), K2O 270 kg x hm(-2), also a larger content of imperatorin and psoralen. The imperatorin content is the largest when applied P2O5 360 kg x hm(-2), K2O 180 kg x hm(-2), and the isoimperatorin content was higher as well. So that the treatment of P2O5 360 kg x hm(-2), K2O 180 kg x hm(-2) are suitable for promote to the agricultural production, which could improve the quality and yield of G. littoralis.

Franck-Condon factors perturbed by damped harmonic oscillators: solvent enhanced X (1)Ag ↔ A(1)B1u absorption and fluorescence spectra of perylene.

Damped harmonic oscillators are utilized to calculate Franck-Condon factors within displaced harmonic oscillator approximation. This is practically done by scaling unperturbed Hessian matrix that represents local modes of force constants for molecule in gaseous phase, and then by diagonalizing perturbed Hessian matrix it results in direct modification of Huang-Rhys factors which represent normal modes of solute molecule perturbed by solvent environment. Scaling parameters are empirically introduced for simulating absorption and fluorescence spectra of an isolated solute molecule in solution. The present method is especially useful for simulating vibronic spectra of polycyclic aromatic hydrocarbon molecules in which hydrogen atom vibrations in solution can be scaled equally, namely the same scaling factor being applied to all hydrogen atoms in polycyclic aromatic hydrocarbons. The present method is demonstrated in simulating solvent enhanced X (1)Ag ↔ A(1)B1u absorption and fluorescence spectra of perylene (medium-sized polycyclic aromatic hydrocarbon) in benzene solution. It is found that one of six active normal modes v10 is actually responsible to the solvent enhancement of spectra observed in experiment. Simulations from all functionals (TD) B3LYP, (TD) B3LYP35, (TD) B3LYP50, and (TD) B3LYP100 draw the same conclusion. Hence, the present method is able to adequately reproduce experimental absorption and fluorescence spectra in both gas and solution phases.

Comparison of Abbott and Da-an real-time PCR for quantitating serum HBV DNA.

AIM: To compare the performance of the Da-an real-time hepatitis B virus (HBV) DNA assay and Abbott RealTime HBV assay. METHODS: HBV DNA standards as well as a total of 180 clinical serum samples from patients with chronic hepatitis B were measured using the Abbott and Da-an real-time polymerase chain reaction (PCR) assays. Correlation and Bland-Altman plot analysis was used to compare the performance of the Abbott and Da-an assays. The HBV DNA levels were logarithmically transformed for analysis. All statistical analyses were performed using SPSS for Windows version 18.0. The correlation between the two assays was analyzed by Pearson's correlation and linear regression. The Bland-Altman plots were used for the analysis of agreement between the two assays. A P value of < 0.05 was considered statistically significant. RESULTS: The HBV DNA values measured by the Abbott or Da-an assay were significantly correlated with the expected values of HBV DNA standards (r = 0.999, for Abbott; r = 0.987, for Da-an, P < 0.001). A Bland-Altman plot showed good agreement between these two assays in detecting HBV DNA standards. Among the 180 clinical serum samples, 126 were quantifiable by both assays. Fifty-two samples were detectable by the Abbott assay but below the detection limit of the Da-an assay. Moreover, HBV DNA levels measured by the Abbott assay were significantly higher than those of the Da-an assay (6.23 ± 1.76 log IU/mL vs 5.46 ± 1.55 log IU/mL, P < 0.001). A positive correlation was observed between HBV DNA concentrations determined by the two assays in 126 paired samples (r = 0.648, P < 0.001). One hundred and fifteen of 126 (91.3%) specimens tested with both assays were within mean difference ± 1.96 SD of HBV DNA levels. CONCLUSION: The Da-an assay presented lower sensitivity and a narrower linear range as compared to the Abbott assay, suggesting the need to be improved.

Aqueous dual-tailed surfactants simulated on the alumina surface.

Atomistic molecular dynamics (MD) simulations were used to compare the morphology of aqueous surfactant self-assembled aggregates on a flat alumina substrate. The substrate was modeled using the CLAYFF force field, and it was considered fully protonated. Three ionic surfactants were considered, all with a sulfate headgroup. The first surfactant was the single-tailed, widely studied sodium dodecyl sulfate (SDS), for which previous simulation results are available on several substrates. The results obtained for this surfactant were used for benchmarking the behavior of two dual-tailed surfactants. These latter surfactants have equal structure, except that in one case both linear tails are composed by seven fully protonated carbon atoms [CH3(CH2)6CHOSO3(CH2)6CH3(-), 2H7], whereas in the other, one tail is composed by seven fully protonated carbon atoms and the other tail is composed by seven fully fluorinated carbon atoms [CF3(CF2)6CHOSO3(CH2)6CH3(-), H7F7]. Our results suggest that preferential interactions lead to surfactant aggregates for H7F7 that differ compared to both those obtained for SDS and 2H7. Although molecular-level geometric structural differences can be invoked to explain differences between H7F7 and SDS aggregates, those between H7F7 and 2H7 aggregates can only be ascribed to atomic-scale interactions. Because as the adsorbed amount of surfactant increases, the self-assembled surfactant aggregates change, suggesting that the substrate on which adsorption occurs effectively evolves as adsorption progresses, compared to bare alumina. The morphological differences observed in our simulations coupled with molecular-level microphase separation might explain, in part, the unusual retrograde adsorption isotherm that has been observed experimentally for H7F7 surfactants on alumina.

Theoretical studies on the mechanism of activation of phosphoprotein phosphatases and purple acid phosphatases suggest an evolutionary strategy to survive in acidic environments.

Dephosphorylation reactions of phosphoprotein phosphatases (PPPs) share a common catalytic cycle. In one stage of the cycle, the active site is regenerated through formation of a new nucleophilic µ-hydroxy moiety and reprotonation of the proton donor, His125 (numbered according to the protein phosphatase 1 sequence). To date the exact details of the mechanism of this step remain uncertain. On the basis of recurring observations in several crystal structures, we propose an activation mechanism in which dephosphorylation of PPPs proceeds mainly through proton transfer from the water molecule that bridges the metal ions to His125, which is mediated by another water molecule. Our calculations using hybrid density functional theory and B3LYP functionals support this activation mechanism. We also propose that Asp95 facilitates proton transfer by eliminating the energy barrier and the backbone carbonyl oxygen atom of His248 acts mainly to orient and stabilize the µ-hydroxo (or water molecule) through hydrogen bonding. Furthermore, on the basis of the structural similarities of the active sites of purple acid phosphatases (PAPs) and PPPs, we speculate that PAPs are activated by a dual proton transfer mediated by one water molecule. Our calculations support this hypothesis and indicate that the active site of PAPs can still be active in an acidic environment (in agreement with the acid phosphatase activity of PAPs). Therefore, the variant of the activation mechanism from PPPs to PAPs implies an evolutionary adaptation to acidic environments.

A new endoscopic ultrasonography image processing method to evaluate the prognosis for pancreatic cancer treated with interstitial brachytherapy.

AIM: To develop a fuzzy classification method to score the texture features of pancreatic cancer in endoscopic ultrasonography (EUS) images and evaluate its utility in making prognosis judgments for patients with unresectable pancreatic cancer treated by EUS-guided interstitial brachytherapy. METHODS: EUS images from our retrospective database were analyzed. The regions of interest were drawn, and texture features were extracted, selected, and scored with a fuzzy classification method using a C++ program. Then, patients with unresectable pancreatic cancer were enrolled to receive EUS-guided iodine 125 radioactive seed implantation. Their fuzzy classification scores, tumor volumes, and carbohydrate antigen 199 (CA199) levels before and after the brachytherapy were recorded. The association between the changes in these parameters and overall survival was analyzed statistically. RESULTS: EUS images of 153 patients with pancreatic cancer and 63 non-cancer patients were analyzed. A total of 25 consecutive patients were enrolled, and they tolerated the brachytherapy well without any complications. There was a correlation between the change in the fuzzy classification score and overall survival (Spearman test, r = 0.616, P = 0.001), whereas no correlation was found to be significant between the change in tumor volume (P = 0.663), CA199 level (P = 0.659), and overall survival. There were 15 patients with a decrease in their fuzzy classification score after brachytherapy, whereas the fuzzy classification score increased in another 10 patients. There was a significant difference in overall survival between the two groups (67 d vs 151 d, P = 0.001), but not in the change of tumor volume and CA199 level. CONCLUSION: Using the fuzzy classification method to analyze EUS images of pancreatic cancer is feasible, and the method can be used to make prognosis judgments for patients with unresectable pancreatic cancer treated by interstitial brachytherapy.

Theoretical studies on the reaction mechanism of PP1 and the effects of different oxidation states of the Mn-Mn center on the mechanism.

Protein phosphatase 1 (PP1) is a dinuclear metalloenzyme that catalyzes the dephosphorylation of serine and threonine residues. In this work, the catalytic reaction mechanism of PP1 was theoretically investigated by hybrid density functional theory. Firstly, an initial model of the Mn(II)-Mn(II) active site of PP1 was constructed on the basis of the high-resolution crystal structure, and stationary points along the reaction pathway were optimized and analyzed. The calculations provide strong support for the mechanism of the dephosphorylation by PP1 and suggest that His125 plays the role of donating a proton to the leaving group. Furthermore, reaction models with the Mn-Mn centers at different oxidation states [Mn(III)-Mn(II) and Mn(III)-Mn(III) centers] were designed. Our calculations show that increasing the oxidation state of one or both Mn(II) can shorten the bond lengths between the metal ions and the ligands, and increase the energy barrier of the related reactions. We found it interesting that artificially adding a negatively charged hydroxy ligand into the Mn(III)-Mn(II) center can recover the shortened coordination bonds and lower the increased energy barrier. Our investigation suggests that the definite oxidation states of the metal centers should be significantly correlated to the negative charges of the ligands not only in phosphoprotein phosphatases, but also in purple acid phosphatases and Escherichia coli 5'-nucleotidase. This means that all the members of phosphoprotein phosphatases adopt homodivalent centers, and suggests the heterovalent active sites of purple acid phosphatases have evolved from homodivalent ones.

Theoretical study of the oxidation of phenolates by the [Cu2O2(N,N'-di-tert-butylethylenediamine)2]2+ complex.

Experiments have shown that the µ-η(2):η(2)-peroxodicopper(II) complex [Cu(2)O(2)(N,N'-di-tert-butylethylenediamine)(2)](2+) rapidly oxidizes 2,4-di-tert-butylphenolate into a mixture of catechol and quinone and that, at the extreme temperature of -120 °C, a bis-µ-oxodicopper(III)-phenolate intermediate, labeled complex A, can be observed. These experimental results suggest a new mechanism of action for the dinuclear copper-containing enzyme tyrosinase, involving an early O-O bond-cleavage step. However, whether phenolate binding occurs before or after the cleavage of the O-O bond has not been possible to answer. In this study, hybrid density functional theory is used to study the synthetic reaction and, based on the calculated free-energy profile, a mechanism is suggested for the entire phenolate-oxidation reaction that agrees with the experimental observations. Most importantly, the calculations show that the very first step in the reaction is the cleavage of the O-O bond in the peroxo complex and that, subsequently, the phenolate substrate coordinates to one of the copper ions in the bis-µ-oxodicopper(III) complex to yield the experimentally characterized phenolate intermediate (A). The oxidation of the phenolate substrate into a quinone then occurs in three steps: 1) C-O bond formation, 2) coupled internal proton and electron transfer, and 3) electron transfer coupled to proton transfer from an external donor (acidic workup, experimentally). The first of these steps is rate limiting for the decay of complex A, with a calculated free-energy barrier of 10.7 kcal mol(-1) and a deuterium kinetic isotope effect of 0.90, which are in good agreement with the experimental values of 11.2 kcal mol(-1) and 0.83(±0.09). The tert-butyl substituents on both the phenol substrate and the copper ligands need to be included in the calculations to give a correct description of the reaction mechanism.

Comparison of the performance of exact-exchange-based density functional methods.

How to describe nondynamic electron correlation is still a major challenge to density functional theory (DFT). Recent models designed particularly for this problem, such as Becke'05 (B05) and Perdew-Staroverov-Tao-Scuseria (PSTS) functionals employ the exact-exchange density, the efficient calculation of which is technically quite challenging. We have recently implemented self-consistently the B05 functional based on an efficient resolution-identity (RI) technique. In this study, we report a self-consistent RI implementation of the PSTS functional. In contrast to its original implementation, our version brings no limitation on the choice of the basis set. We have also implemented the Mori-Sanchez-Cohen-Yang-2 (MCY2) functional, another recent DFT method that includes full exact exchange. The performance of PSTS, B05, and MCY2 is validated on thermochemistry, reaction barriers, and dissociation energy curves, with an emphasis on nondynamic correlation effects in the discussion. All three methods perform rather well in general, B05 and MCY2 being on average somewhat better than PSTS. We include also results with other functionals that represent various aspects of the development in this field in recent years, including B3LYP, M06-HF, M06-2X, ωB97X, and TPSSh. The performance of the heavy-parameterized functionals M06-2X and ωB97X is on average better than that of B05, MCY2, and PSTS for standard thermodynamic properties and reactions, while the latter functionals do better in hydrogen abstraction reactions and dissociation processes. In particular, B05 is found to be the only functional that yields qualitatively correct dissociation curves for two-center symmetric radicals like He(2)(+). Finally, we compare the performance of all these functionals on a strongly correlated exemplary case system, the NO dimer. Only PSTS, B05, and MCY2 describe the system qualitatively correctly. Overall, this new type of functionals show good promise of overcoming some of the difficulties DFT encounters for systems with strong nondynamic correlation.

Mechanistic insight into the N=N bond-cleavage of azo-compounds that was induced by an Al-Al-bonded compound [L(2-)Al(II)-Al(II)L(2-)].

An α-diimine-stabilized Al-Al-bonded compound [L(2-)Al(II)-Al(II)L(2-)] (L = [{(2,6-iPr(2)C(6)H(3))NC(Me)}(2)]; 1) consists of dianionic α-diimine ligands and sub-valent Al(2+) ions and thus could potentially behave as a multielectron reductant. The reactions of compound 1 with azo-compounds afforded phenylimido-bridged products [L(-)Al(III)(µ(2)-NPh)(µ(2)-NAr)Al(III)L(-)] (2-4). During the reaction, the dianionic ligands and Al(2+) ions were oxidized into monoanions and Al(3+), respectively, whilst the [NAr](2-) imides were produced by the four-electron reductive cleavage of the N=N double bond. Upon further reduction by Na, the monoanionic ligands in compound 2 were reduced to the dianion to give [(L(2-))(2)Al(III)(2)(µ(2)-NPh)(2)Na(2)(thf)(4)] (5). Interestingly, when asymmetric azo-compounds were used, the asymmetric adducts were isolated as the only products (compounds 3 and 4). DFT calculations indicated that the reaction was quite feasible in the singlet electronic state, but the final product with the triplet-state monoanionic ligands could result from an exothermic singlet-to-triplet conversion during the reaction process.

Theoretical studies of chromophore maturation in the wild-type green fluorescent protein: ONIOM(DFT:MM) investigation of the mechanism of cyclization.

The availability of a gene encoding green fluorescence immediately stimulates interest in the puzzle of autocatalytic formation of the green fluorescent protein (GFP) chromophore. Numerous experimental and theoretical studies have indicated that cyclization is the first and most important step in the maturation process of the GFP. In our previous paper based on cluster models [J. Phys. Chem. B2010, 114, 9698-9705], two possible mechanisms have been investigated with the conclusion that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 α-carbon. However, the impact of the protein environment on the reaction mechanism remains to be explored. In this paper, we investigated the two possible mechanisms with inclusion of protein environmental effects by using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Our calculations reveal no hydrogen bonding network that would facilitate deprotonation of the amide nitrogen of Gly67, although it is the lower energy pathway in the cluster model system. Contrastingly, there is a hydrogen bonding network between Tyr66 α-carbon and Glu222, which is in good agreement with X-ray data. The ONIOM studies show that proton transfer from Tyr66 α-carbon to Glu222 is a long-distance charge transfer process. The charge distribution of the MM region has a significant perturbation to the wave function for the QM region, with the QM energy for the proton transfer product being increased under the influence of the electrostatic protein environment. The barrier for the rate-limiting step in cyclization is quite high, about 40.0 kcal/mol in the case of ONIOM-EE.

UV-spectroscopy, electronic structure and ozonolytic reactivity of sesquiterpenes: a theoretical study.

Sesquiterpenes, one of the most important classes of biogenic volatile organic compounds, are potentially significant precursors to secondary organic aerosols (SOAs) in nature. The electronic structure of sesquiterpenes and their reactivity in the ozonolysis reaction were investigated by density functional theory. Results from the CIS calculations combined with an analysis of transition intensities show that the first peaks in the ultraviolet (UV) spectra for saturated and unsaturated isomers are σ-σ and π-π transitions, respectively. The UV absorption wavelength and absorbency are dictated by the electronic structures of these compounds. An increase in the number of double bonds and formation of a conjugated system expand the range of absorption in the UV region. An isomer with an endocyclic C = C bond presents weaker UV transition intensity than its corresponding exocyclic isomer. Results from conceptual DFT chemical reactivity indices of isomers suggest that no quantitative linear relationships between the structural changes and their reactivity, such as different degrees of unsaturated C = C double bonds, or the number of substituents attached to the C = C bond were discovered. In the ozonolysis reaction of sesquiterpenes, isomers with larger steric hindrance of substituents or endocyclic C = C bond possess higher chemical reactivity compared to isomers with smaller steric hindrandce or with an exocyclic C = C bond. These results are imperative to a better understanding of SOAs production mechanisms in the troposphere.