Effect of Interfacial Action on the Generation and Transformation of Reactive Oxygen Species in Tripolyphosphate-Enhanced Heterogeneous Fe3O4/O2 Systems.

It has been reported that tripolyphosphate (TPP) can enhance the oxygenation of natural Fe(II)-containing minerals to produce reactive oxygen species (ROS). However, the molecular structure of the TPP-Fe(II) mineral surface complex and the role of this complex in the generation and transformation of ROS have not been fully characterized. In the present study, a heterogeneous magnetite (Fe3O4)/O2/TPP system was developed for the degradation of p-nitrophenol (PNP). The results showed that the addition of TPP significantly accelerated the removal of PNP in the Fe3O4/O2 system and extended the range of effective pH to neutral. Experiments combined with density functional theory calculations revealed that the activation of O2 mainly occurs on the surface of Fe3O4 induced by a structural Fe(II)-TPP complex, where the generated O2•- (intermediate active species) can be rapidly converted into H2O2, and then the •OH generated by the Fenton reaction is released into the solution. This increases the concentration of •OH produced and the efficiency of •OH produced relative to Fe(II) consumed, compared with the homogeneous system. Furthermore, the binding of TPP to the surface of Fe3O4 led to stretching and even cleavage of the Fe-O bonds. Consequently, more Fe(II)/(III) atoms are exposed to the solvation environment and are available for the binding of active O2 and O2•-. This study demonstrates how common iron minerals and O2 in the natural environment can be combined to yield a green remediation technology.

Investigating the influence of substituent groups in TTM based radicals for the excitation process: a theoretical study.

Tri-(2,4,6-trichlorophenyl)methyl (TTM) based radicals can be promising in providing relatively high fluorescence quantum efficiency. In this study, we have evaluated the photoluminescence properties of a series of TTM-based radicals by means of DFT and TD-DFT methods. The optimized structures of the ground states (D0) and the first excited states (D1) of all the radicals are calculated and the computed emission bands are comparable with previous experimental results. knr is determined from transition dipole moments (µ12) and the energy gaps between D0 and D1 (ΔE), both of which can be regulated by the conjugated structures from the substituent groups. knr was derived from the mode-averaging method and is consistent with the experimental results. Factors influencing kr and knr, including the potential energy differences (ΔG0), the vibrational reorganization energies (λ) and the electron coupling term (Hab), are discussed. By comparing kr and knr in solvents with different polarities (cyclohexane, toluene, and chloroform), TTM based radicals in cyclohexane exhibit the most promising fluorescence efficiencies. Besides, two substituted radicals, namely 2Br-TTM-3PCz and 2F-TTM-3PCz, have been fabricated. The results show that fluorine atoms are able to increase ΔG0 and a considerably small knr has been predicted. We expect that our calculation can benefit the design of light-emitting molecules in further experiments.

Generation of Reactive Oxygen Species and Degradation of Pollutants in the Fe2+/O2/Tripolyphosphate System: Regulated by the Concentration Ratio of Fe2+ and Tripolyphosphate.

Tripolyphosphate (TPP) has many advantages as a ligand for the optimization of the Fe2+/O2 system in environmental remediation applications. However, the relationship between remediation performance and the Fe2+/TPP ratio in the system has not been previously described. In this study, we report that the degradation mechanism of p-nitrophenol (PNP) in Fe2+/O2 systems is regulated by the Fe2+/TPP ratio under neutral conditions. The results showed that although PNP was effectively degraded at different Fe2+/TPP ratios, the results of specific reactive oxygen species (ROS) scavenging experiments and the determination of PNP degradation products showed that the mechanism of PNP degradation varies with the Fe2+/TPP ratio. When CFe2+ ≥ CTPP, the initially formed O2•- is converted to •OH and the •OH degrades PNP by oxidation. However, when CFe2+ < CTPP, the O2•- persists long enough to degrade PNP by reduction. Density functional theory (DFT) calculations revealed that the main reactive species of Fe2+ in the system include [Fe(TPP)(H2O)3]- and [Fe(TPP)2]4-, whose content in the solution is the key to achieve system regulation. Consequently, by controlling the Fe2+/TPP ratio in the solution, the degradation pathways of PNP can be selected. Our study proposed a new strategy to regulate the oxidation/reduction removal of pollutants by simply varying the Fe2+/TPP ratio of the Fe2+/O2 system.

Investigating detailed mechanism of hydrogen molecules adsorbing on single-wall carbon nanotubes using fitted force field parameters containing carbon-carbon interactions.

The nonbonded and bonded force field parameters for carbon atoms in single-wall carbon nanotubes (SWNT) are fitted by means of quantum chemistry calculations with considering the periodic boundary conditions. The nonbonded parameters between carbon atoms and hydrogen atoms are fitted as well. All the fitted parameters are verified by comparing to quantum chemistry results and by calculating Young's modulus. Adsorption of Hydrogen molecules are then carried out on a bundle of self-assembled SWNTs. The adsorption isotherms are consistent to the Freundlich equation. Both hydrogen molecules adsorbed outside and inside the SWNTs are counted. According to our result, hydrogen molecules adsorbed inside the SWNTs are more stable at a relatively high temperature and are playing an important part in total amount of the adsorbed molecules. While C(10,10) have the highest adsorption capacities in most of the temperatures, hydrogen molecules inside C(5,5) are the most stable of all the four kinds of SWNTs. Thus, balancing adsorption capacities and strength of interaction can be important in choosing SWNT for gas adsorption. Besides, we deduct an equation that can describe the relation between hydrogen pressure and amount of SWNTs based on our simulation results. The hydrogen pressure may decrease by adding SWNTs in the system. The fitting method in our system is valid to SWNTs and can be tested in further studies of similar systems. © 2018 Wiley Periodicals, Inc.

Theoretical analysis of electrochromism under redox of bis(3-thienyl)/(2-thienyl)hexafluorocyclopentene: effects of charged and substituted systems.

Electrochromism with the ring-closing or ring-opening isomerization of substituted and unsubstituted bis(3-thienyl)/(2-thienyl)hexafluorocyclopentene is discussed using the DFT method. In the neutral ground state, bond making and breaking between two reactive C atoms on thienyls are thermodynamically forbidden. Under redox conditions, the gain or loss of electrons can have a significant effect on the frontier molecular orbital distribution of both open- and closed-ring isomers, particularly in reactive sites. Corresponding structural changes show a trend toward isomerization. The reaction energy barrier shows greater reduction for dication than monocation and even becomes barrierless for dianion. During the isomerization in different states, the conjugated system switches distinctively, which is attributed to the special redistribution of molecular orbitals and spin population in each state. In monocation and monoanion, for the involvement of a single electron, isomerization is inclined to proceed sequentially between right and left thienyls, whereas it becomes synchronous in dication. The direction depends on the stabilization achieved by the formation of a global conjugated system and more average spin population on the molecule. The effect of substituents on thienyls is demonstrated in the promotion of the extent of conjugation and the determination of the spin population level on the reactive C atoms. Moreover, according to their electron-donating and withdrawing abilities, they can kinetically support or suppress the electron transfer pattern in the process from isomer to transition state, which leads to the control of reaction efficiency.

Structural features and dynamic investigations of the membrane-bound cytochrome P450 17A1.

Cytochrome P450 (CYP) 17A1 is a dual-function monooxygenase with a critical role in the synthesis of many human steroid hormones. The enzyme is an important target for treatment of breast and prostate cancers that proliferate in response to estrogens and androgens. Despite the crystallographic structures available for CYP17A1, no membrane-bound structural features of this enzyme at atomic level are available. Accumulating evidence has indicated that the interactions between bounded CYPs and membrane could contribute to the recruitment of lipophilic substrates. To this end, we have investigated the effects on structural characteristics in the presence of the membrane for CYP17A1. The MD simulation results demonstrate a spontaneous insertion process of the enzyme to the lipid. Two predominant modes of CYP17A1 in the membrane are captured, characterized by the depths of insertion and orientations of the enzyme to the membrane surface. The measured heme tilt angles show good consistence with experimental data, thereby verifying the validity of the structural models. Moreover, conformational changes induced by the membrane might have impact on the accessibility of the active site to lipophilic substrates. The dynamics of internal aromatic gate formed by Trp220 and Phe224 are suggested to regulate tunnel opening motions. The knowledge of the membrane binding characteristics could guide future experimental and computational works on membrane-bound CYPs so that various investigations of CYPs in their natural, lipid environment rather than in artificially solubilized forms may be achieved.

Investigation of properties of Mg(n) clusters and their hydrogen storage mechanism: a study based on DFT and a global minimum optimization method.

The global minimum structures of Mgn clusters have been determined using the so-called "kick method". With the improved DFT method of B3PW91 functional and Grimme's dispersion correction, a series of the most stable structure of Mgn have been found and a novel Mg9 structure has been located. Subsequently, the chemisorption of hydrogen onto Mg clusters was systemically studied. Considering the average adsorption energies and the ratio of Mg and H, we developed a function that can describe the relation between average adsorption energy and number of Mg and H atoms. Our results may be helpful in the future for developing different kinds of gas chemisorption materials.

The molecular configuration of a DOPA/ST monolayer at the air-water interface: a molecular dynamics study.

In this study, surface pressure-area isotherms for N-stearoyldopamine (DOPA) and 4-stearylcatechol (ST) monolayers are obtained by means of molecular dynamics simulations and compared to experimental isotherms. The difference between DOPA and ST is an amide group, which is present in the alkyl tails of DOPA molecules. We find a large difference between the isotherms for DOPA and ST monolayers. Upon using TIP4P/2005 for water and OPLS force fields for the organic material and a relatively large system size, the simulated results are found to be consistent with experiments. With molecular dynamics simulations, the configurations of molecules in the monolayers can be directly analyzed. When the surface pressure is high, a regular molecular orientation is observed for ST molecules, whereas regular orientations are only observed in local domains for DOPA molecules. The differences between DOPA and ST monolayers are attributed to the amide groups in DOPA molecules, which are useful for both steric effects and the formation of hydrogen bonds in the DOPA monolayers. This study clearly demonstrates that hydrogen bonds, due to the presence of the amide group in DOPA, are the cause of the disorder in its Langmuir monolayers. Thus, the conclusion may be helpful in making ordered organic monolayers in the future.

Molecular dynamics simulation of a DOPA/ST monolayer on the Au(111) surface.

In order to study the influence of molecular structure on the formation of a monolayer, two molecules have been considered, namely N-stearoyldopamine (DOPA) and 4-stearyl-catechol (ST). The difference between these two molecules is the amide group in DOPA. By investigating these monolayers at different surface areas per molecule, the molecular configurations of a DOPA/ST monolayer on the Au(111) surface were obtained. We conclude that for both kinds of molecules, the π-interaction between the catechol group and the Au(111) surface is important. Compared to experimental results, the catechol groups are found either parallel or perpendicular to the Au(111) surface in MD simulation. The difference between DOPA and ST systems is that when there are fewer molecules on the Au(111) surface, in the DOPA system, the amount of catechol groups perpendicular with their hydroxyls orienting towards the surface is less than that of the ST system. Further analysis of catechol groups and amide groups indicates that various kinds of hydrogen bonds formed in the DOPA system have a profound influence on the structure and regularity of the monolayer.

Design and bioanalytical applications of stochastic DNA walkers.

Synthetic DNA walkers that are inspired by the walking behaviors of naturally occurring motor proteins have emerged into an important subfield of DNA nanotechnology. While early DNA walkers were designed to walk on one-dimensional (1D) DNA tracks, the development of DNA origami and DNA functionalized micro-/nanomaterials has enabled diverse 2D and 3D tracks. Random walking becomes possible in such platforms and such stochastic DNA walkers can be engineered with much-improved speed and processivity. The invention and improvement of diverse stochastic DNA walkers have made them ideal amplification platforms for analytical and diagnostic applications. In this feature article, we first review the development of DNA walkers with a historical aspect and then focus on the advances in stochastic DNA walkers. We finally elaborated our research efforts to design varying 3D stochastic DNA walkers for rapid and amplified detection of biologically important nucleic acids and proteins.

Theoretical insight on the saturated stimulated emission intensity of a squaraine dye for STED nanoscopy.

Stimulated emission depletion nanoscopy (STED) is increasingly applied for the insights into the ultra-structures of organelles in live cells because of the bypassing of the Abbe's optical diffraction limit. Theoretically, with the increase of excitation and depletion laser power, the imaging resolution can be accordingly enhanced and even close to the infinity. Unfortunately, powerful laser illuminations usually produce severe phototoxicity and photobleaching, which will lead to more extra-interference with biological events in live cells and accelerate the decomposition of the fluorescent probes. In view of the trade-off of cell viability and imaging resolution, excellent probes with superior photophysical properties are great in demand. For a qualified STED probes, the saturated stimulated emission intensity (Isat) is considered as a key evaluating factor. According to the formula, Isat is inversely proportional to the stimulated emission cross section (σsti) of the fluorescent probe. However, the relationship between the σsti and chemical structure of the STED probe remain to be unclear. In this work, we explore the influence factors by theoretical calculations on a squaraine dye (MitoEsq-635) and a commercial dye (Atto647N). The results indicate that the increase of transition dipole moment (µ) are beneficial for the increase of σsti, thereafter reducing Isat. Furthermore, we firstly proposed that stimulated emission depletion was qualitatively interpreted by the investigation on the potential energy surfaces of ground states (S0) and the first excited states (S1) of the dyes.

Stimuli-Responsive Three-Dimensional DNA Nanomachines Engineered by Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces.

Stimuli-responsive nanomachines are attractive tools for biosensing, imaging, and drug delivery. Herein, we demonstrate that the orientation of macromolecules and subsequent dynamic interactions at the biomolecule-nanoparticle (bio-nano) interfaces can be rationally controlled to engineer stimuli-responsive DNA nanomachines. The success of this design principle was demonstrated by engineering a series of antibody-responsive DNA walkers capable of moving persistently on a three-dimensional track made of DNA functionalized gold nanoparticles. We show that drastically different responses to antibodies could be achieved using DNA walkers of identical sequences but with varying number or sites of modifications. We also show that multiple interfacial factors could be combined to engineer stimuli-responsive DNA nanomachines with high sensitivity and modularity. The potential of our strategy for practical uses was finally demonstrated for the amplified detection of antibodies and small molecules in both buffer and human serum samples. Unlike many DNA-based nanomachines, the performance of which could be significantly hindered by the matrix of serum, our system shows a matrix-enhanced sensitivity as a result of the engineering approach at the bio-nano interface.

Investigating phosphorescence capability of halogen-substituted metal-free organic molecules: A theoretical study.

The radiative and non-radiative decay processes of five compounds are investigated through a comprehensive computational approach, for the aim of investigating the effect of different halogen substituents to the phosphorescent emission. Their optimal configurations at the ground (S0) and lowest triplet excited (T1) states are obtained and the calculated phosphorescent emission spectra are comparable with the experimental values. For 1,4-di(9H-carbazol-9-yl)benzene (PDCz), the electronic transition is between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), while for the four halides, the electronic transitions are attributed to several molecular orbitals. According to calculations, 9,9'-(2,5-diiodo-1,4-phenylene)bis(9H-carbazole) (PDICz) possesses the largest radiative decay rate constant (kr) and non-radiative decay rate constant (knr), which can be attributed to the strong spin-orbital coupling from the heavy iodine atom. However, the phosphorescent quantum efficiency (Φ) of PDICz is lower than that of 9,9'-(2,5-dibromo-1,4-phenylene)bis(9H-carbazole) (PDBCz), implying that a comprehensive consideration is necessary. Furthermore, by analyzing the vibrational mode, we have confirmed that the reorganization energies are also influenced by the different halogen atoms. While the dominated factor that determines the kr and knr comes from the spin-orbital coupling. We expect that our research findings will be beneficial to the newly designed organic phosphorescent materials in the future.

Sensing mechanism of a fluorescent probe for thiophenols: Invalidity of excited-state intramolecular proton transfer mechanism.

Simple and effective detection of thiophenols has attracted great attention. A fluorescent probe 1 with high selectivity and sensitivity is designed and synthesized based on the excited-state intramolecular proton transfer (ESIPT) in experiment. However, we conclude that the ESIPT process fails to happen actually based on the calculation results. In the present work, the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods are employed to investigate the real sensing mechanism. The calculated absorption and emission spectra agree well with the experimental results. By comparing the energy of enol and keto configurations and the constructed potential energy surfaces (PESs) in the ground (S0) and excited (S1) states of 3-(benzo[d]thiazol-2-yl)-10-butyl-10H-phenothiazin-2-ol (dye 2), the ESIPT process is confirmed impossible because of the relatively high keto form energy and potential energy barrier. Besides, the transition state of dye 2 is optimized to offer the accurate potential energy barrier. The results of calculated frontier molecular orbitals (FMOs) and spectra indicate that it is the photoinduced electron transfer (PET) process that results in the fluorescence quenching of probe 1. After adding thiophenols, the thiolysis of 2,4-dinitrophenyl ether bond is triggered and dye 2, which emits strong fluorescence because of the absence of PET process, is obtained. Consequently, our study has demonstrated that probe 1 can act as a fluorescent probe to detect thiophenols through the off-on fluorescence variation based on the PET mechanism but not the ESIPT process.

A novel T-C3N and seawater desalination.

A structurally stable stacked multilayer carbonitride is predicted with the aid of ab initio calculations. This carbonitride consists of C3N tetrahedra, and is similar to T-carbon and thus named T-C3N. Its 2-dimensional (2D) monolayer is also carefully investigated in this work. The studies on electronic properties reveal that bulk and 2D T-C3N are insulators with a 5.542 eV indirect band gap and a 5.741 eV direct band gap, respectively. However, the monolayer T-C3N exhibits an excellent uniform porosity. Its 5.50 Å pore size is perfect for water nanofiltration. The adsorption and permeation of water molecules on the monolayer T-C3N are investigated. Its promising potential application in highly efficient nanofiltration membranes for seawater desalination is discussed.

Repetitive exposure to low-dose X-irradiation attenuates testicular apoptosis in type 2 diabetic rats, likely via Akt-mediated Nrf2 activation.

To determine whether repetitive exposure to low-dose radiation (LDR) attenuates type 2 diabetes (T2DM)-induced testicular apoptotic cell death in a T2DM rat model, we examined the effects of LDR exposure on diabetic and age-matched control rats. We found that testicular apoptosis and oxidative stress levels were significantly higher in T2DM rats than in control rats. In addition, glucose metabolism-related Akt and GSK-3ß function was downregulated and Akt negative regulators PTP1B and TRB3 were upregulated in the T2DM group. Superoxide dismutase (SOD) activity and catalase content were also found to be decreased in T2DM rats. These effects were partially prevented or reversed by repetitive LDR exposure. Nrf2 and its downstream genes NQO1, SOD, and catalase were significantly upregulated by repetitive exposure to LDR, suggesting that the reduction of T2DM-induced testicular apoptosis due to repetitive LDR exposure likely involves enhancement of testicular Akt-mediated glucose metabolism and anti-oxidative defense mechanisms.

Heparin makes differences: a molecular dynamics simulation study on the human ßII-tryptase monomer.

Human ß-tryptase, an enzyme with trypsin-like activity in mast cells, is an important target for the treatment of inflammatory and allergy related diseases. Heparin has been inferred to play a vital role in the stabilization of the tryptase structure and the maintenance of its active form. Up to now, the structure-function relationship between heparin and the ßII-tryptase monomer has not been studied with atomic resolution due to the lack of a complex structure of tryptase and heparin. To this end, the exact effect of heparin bonding to the ßII-tryptase monomer structure has been investigated using molecular docking and molecular dynamics (MD) simulation. The MD simulation results combined with MM-GB/SA calculations showed that heparin stabilized the ß-tryptase structure mainly through salt bridge interaction. The averaged noncovalent interaction (aNCI) method was employed for the visualization of nonbonding interactions. A crucial loop, which is located in the core region of ßII-tryptase monomer structure, has been found. Arg188 and Asp189 from this loop act as a salt bridge intermediary between 4-mer heparin and 0GX. The observation of a salt bridge between Asp189 and P1 groups of 0GX confirms the supposed interaction between these two groups. These two residues have been proved to be responsible for the direction of the P1 group of 0GX. Our study revealed that how heparin affected the activity of the human ßII-tryptase monomer (hBTM) through salt bridge interactions. The knowledge of heparin binding characteristics and the key residue contributions in this study may enlighten further the inhibitor design of this enzyme and may also improve our understanding of inflammatory and allergy related diseases.

Mechanism of a pH-induced peptide inserting into a POPC bilayer: a molecular dynamic study.

Membrane insertion peptides have been developed in recent years and serve as cargos to deliver small molecules into cells. A class of membrane insertion peptides is the so called pH-induced peptides (pHLIPs), which are able to insert into membrane when the environment pH is acidic. Despite a number of experimental studies, the insertion process as well as the penetration mechanism is still worth study with computational methods. Thus, we performed molecular dynamics simulations in this study to elucidate the detailed penetration process and mechanism. Both protonated and unprotonated peptides are employed to interact with a POPCs bilayer. By analyzing the trajectory of the simulation, the peptide travelling across membrane is expected to take milliseconds or seconds. While the peptide penetrating through the POPC bilayer boundary is much faster (several nanoseconds). More importantly, the elaborate energies between a peptide and water molecules, the energies between a peptide and POPCs have been analyzed throughout the simulation time correspondingly. A constant decrease of interaction energies have been observed for peptide-water interaction in the protonated condition. At last, we employ the statistics of hydrogen bonds to explain the penetration mechanism tentatively. For the protonated system, the decrease of hydrogen bonds of peptide-water and the increase of hydrogen bonds of peptide- POPCs have been considered as the main driven force for the peptide insertion.

Enhanced fluoride adsorption using Al (III) modified calcium hydroxyapatite.

Aluminum-modified hydroxyapatite (Al-HAP) was prepared and characterized using XRD and BET analyses. Al-HAP possessed higher defluoridation capacity (DC) of 32.57 mgF(-)/g than unmodified hydroxyapatite (HAP) which showed a DC of 16.38 mgF(-)/g. The effect of Al/Ca atomic ratio in Al-HAP, solution pH and co-existing anions was further studied. The results indicated that the adsorption data could be well described by the Langmuir isotherm model and the adsorption kinetic followed the pseudo-second-order model. The pH changes during the adsorption process suggested that the OH on the surface of Al-HAP was the adsorption sites. The more adsorption sites were formed on Al modified HAP, which possessed abundant surface hydroxyl groups, resulting in higher efficiency of F(-) removal. Thermodynamic parameters such as ΔG°, ΔH° and ΔS° were calculated in order to understand the nature of adsorption process. The results revealed that the adsorption reaction was a spontaneous and endothermic process.