Transformation of Diffusion and Local Structure of CH4 , CO2 , SO2 and H2 O Mixtures in Graphene Under Wide Temperature and Pressure Range: A Molecular Dynamics Simulation Study.

As a material with high specific surface area and excellent chemical stability, graphene exhibited remarkable adsorption and separation performance as well as a wide range of potential applications. The graphene layer played a significant role in influencing gas transmission. In this study, we employed molecular dynamics simulation to investigate the diffusion characteristics and local structures of a mixed system consisting of CH4 , CO2 , SO2 and H2 O. Additionally, we further examined the transformation of the behavior of these mixtures within graphene layers. The order of diffusion coefficients of the four molecules without graphene was H2 O>SO2 >CO2 ≫CH4 . However, in the double-layer graphene, the order changed to CH4 >CO2 ≫H2 O>SO2 . Higher temperatures and lower pressures were found to facilitate gas diffusion. Temperature and pressure had great effects on the local structures of CH4 , CO2 and SO2 , while their impact on H2 O was limited due to the extensive network of hydrogen bonds formed by H2 O molecules. The statistical results of average coordination number revealed that CH4 tended to aggregate with itself, whereas CO2 and SO2 exhibited a tendency to aggregate with H2 O. The graphene structure enhanced the separation and transportation of CH4 from mixed systems.

Boosting Li-O2 Battery Performance via Coupling of P-N Site-Rich N, P Co-Doped Graphene-Like Carbon Nanosheets with Nano-CePO4.

Development of efficient and robust cathode catalysts is critical for the commercialization of Li-O2 batteries (LOBs). Herein, a well-designed CePO4 @N-P-CNSs cathode catalyst for LOBs via coupling P-N site-rich N, P co-doped graphene-like carbon nanosheets (N-P-CNSs) with nano-CePO4 via a novel "in situ derivation" coupling strategy by in situ transforming the P atoms of P-C sites in N-P-CNSs to CePO4 is reported. The CePO4 @N-P-CNSs exhibit superior bifunctional ORR/OER activity relative to commercial Pt/C-RuO2 with an overall overpotential of 0.64 V (vs RHE). Moreover, the LOB with CePO4 @N-P-CNSs as the cathode catalyst delivers a low charge overpotential of 0.67 V (vs Li/Li+ ), high discharge capacity of 29774 mAh g-1 at 100 mA g-1 and long cycling stability of 415 cycles, respectively. The remarkably enhanced LOB performance is attributable to the in situ derived CePO4 nanoparticles and the P-N sites in N-P-CNSs, which facilitate increased bifunctional ORR/OER activity, promote the rapid and effective decomposition of Li2 O2 and inhibit the formation of Li2 CO3 . This work may provide new inspiration for designing efficient, durable, and cost-effective cathode catalysts for LOBs.

A new 1,2,3-triazole and its rhodamine B derivatives as a fluorescence probe for mercury ions.

A newly synthesized compound, 5-methyl-1-phenyl-1H-1,2,3-triazole-4- carboxylic acid (MPC) was analyzed for its quantum chemical parameters and theoretical spectrum by computational chemistry. The calculated spectrum was in accord with the experimental measurements in a great degree. Then MPC was successfully designed and synthesized to a novel rhodamine B derivative RMPC. The RMPC exhibited about a 4000-fold increase in fluorescence intensity in the presence of Hg2+ ions over most other competitive metal ions. The triazole appended colorless chemodosimeter RMPC turns to pink upon the complex formation only with Hg2+ ions as a 1: 2 M ratio and enables naked-eye detection. The coordination mechanism of turning on/off fluorescence for Hg2+ ions were well proposed by explaining Hg2+ inducing the ring-opened rhodamine B moiety. The fluorescence imaging experiments of Hg2+ in HeLa cell demonstrated that the probe was labeled and it could be used in biological systems.

From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective.

The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism, especially the sequence dependence for the formation of varied chromatin structures in different cells remains to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI (CpG island) forest and prairie genomic domains based on CGI densities of a species, dividing the genome into two sequentially, epigenetically, and transcriptionally distinct regions. These two megabase-sized domains also spatially segregate to different extents in different cell types. Forests and prairies show enhanced segregation from each other in development, differentiation, and senescence, meanwhile the multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, helping to define cell identity. We propose that the phase separation of the 1D mosaic sequence in space serves as a potential driving force, and together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types. The mosaicity in genome of different species in terms of forests and prairies could relate to observations in their biological processes like development and aging. In this way, we provide a bottoms-up theory to explain the chromatin structural and epigenetic changes in different processes.

Molecular dynamics simulation of diffusion coefficients and structural properties of some alkylbenzenes in supercritical carbon dioxide at infinite dilution.

The binary infinite dilute diffusion coefficients, D12(∞), of some alkylbenzenes (Ph-C(n), from Ph-H to Ph-C12) from 313 K to 333 K at 15 MPa in supercritical carbon dioxide (scCO2) have been studied by molecular dynamics (MD) simulation. The MD values agree well with the experimental ones, which indicate MD simulation technique is a powerful way to predict and obtain diffusion coefficients of solutes in supercritical fluids. Besides, the local structures of Ph-C(n)/CO2 fluids are further investigated by calculating radial distribution functions and coordination numbers. It qualitatively convinces that the first solvation shell of Ph-C(n) in scCO2 is significantly influenced by the structure of Ph-C(n) solute. Meanwhile, the mean end-to-end distance, the mean radius of gyration and dihedral angle distribution are calculated to gain an insight into the structural properties of Ph-C(n) in scCO2. The abnormal trends of radial distribution functions and coordination numbers can be reasonably explained in term of molecular flexibility. Moreover, the computed results of dihedral angle clarify that flexibility of long-chain Ph-C(n) is the result of internal rotation of C-C single bond (σ(c-c)) in alkyl chain. It is interesting that compared with n-alkane, because of the existence of benzene ring, the flexibility of alkyl chain in Ph-C(n) with same carbon atom number is significantly reduced, as a result, the carbon chain dependence of diffusion behaviors for long-chain n-alkane (n ≥ 5) and long-chain Ph-C(n) (n ≥ 4) in scCO2 are different.

Evolution of self-diffusion and local structure in some amines over a wide temperature range at high pressures: a molecular dynamics simulation study.

Self-diffusion and structural properties of ammonia, methylamine and trimethylamine have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 700 K at pressures up to 400 MPa. The calculation results agree well with the experiment, which suggests that one can use the simulation method as a powerful tool to obtain self-diffusion coefficients over wide range of temperatures and pressures, under which it is rather difficult for experiments. The local structures of such fluids are investigated by calculating radial distribution functions (RDFs), the numbers of hydrogen bonds and coordination numbers. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The simulation results demonstrate that the temperature effects are more pronounced than the pressure effects on self-diffusion and structural properties, and the effect of hydrogen bonding on the translational dynamics in any of these systems is a minor factor, while it is mainly affected by the close packing of amine molecules.

The study on the interactions of two 1,2,3-triazoles with several biological macromolecules by multiple spectroscopic methodologies and molecular docking.

1-(4-chlorophenyl)-5-phenyl-1H-1,2,3-triazole (CPTC) and 5-(3-chlorophenyl) -1-phenyl-1H-1,2,3-triazole (PCTA) are two new derivatives of 1,2,3-triazole. Their structural and spectral properties were characterized by density functional theory calculations (DFT). The binding properties of CPTC or PCTA with several typical biomacromolecules such as human serum albumin (HSA), bovine hemoglobin (BHb), human immunoglobulin (HIgG) or DNA were investigated by molecular docking and multiple spectroscopic methodologies. The different parameters including binding constants and thermodynamic parameters for CPTC/PCTA-HSA/BHb/HIgG/DNA systems were obtained based on various fluorescence enhancement or quenching mechanisms. The results of binding constants indicated that there were the strong interactions between two triazoles and four biological macromolecules due to the higher order of magnitude between 103 and 105. The values of thermodynamic parameters revealed that the binding forces for these systems are mainly hydrophobic interactions, electrostatic force, or hydrogen bond, respectively, which are in agreement with the results of molecular docking to a certain extent. Moreover, the information from synchronous, 3D fluorescence and UV-Vis spectroscopies proved that two compounds CPTC and PCTA could affect the microenvironment of amino acids residues of three kinds of proteins. Based on the above experimental results, a comparison of the interaction mechanisms for CPTC/PCTA-proteins/DNA systems have been performed in view of their different molecular structures, which is beneficial for the further research in order to design them as the novel drugs.

The computational and experimental studies on a 1, 2, 3-triazole compound and its special binding to three kinds of blood proteins.

A newly synthesized compound, ethyl 5-phenyl-2-(p-tolyl)-2H-1, 2, 3-triazole-4-carboxylate (EPPC) may be considered as a drug candidate and was exploited to study the structural and spectral properties by using quantum chemical calculation and multiple spectroscopic techniques. The results on theoretical spectrum of EPPC were consistent with experimental spectrum in great degree. In addition, EPPC has been as a special probe and investigated on the interactions with three kinds of blood proteins including human serum albumin (HSA), human immunoglobulin (HIgG) and bovine hemoglobin (BHb) by using UV-Vis, fluorescence spectroscopy and molecular modeling, respectively. Changes in various fluorescence and UV-Vis spectra were observed upon ligand binding along with a remarkable degree of fluorescence enhancement on complex formation under physiological condition with binding constant about 105 order of magnitudes, which caused the variations of conformation and microenvironment of these proteins in aqueous solution. The obtained results from the thermodynamic parameters calculated according to the van't Hoff equation indicated that the entropy change ΔS° and enthalpy change ΔH° were found to be 0.168 KJ/mol K and 22.154 KJ/mol for EPPC-HSA system, 0.284 KJ/mol K and 54.408 KJ/mol for EPPC-HIgG system, and 0.228 KJ/mol K and 37.548 KJ/mol for EPPC-BHb system, respectively, which demonstrated that the primary binding pattern is determined by hydrophobic interaction. The results of docking and molecular dynamics simulation using three proteins crystal models revealed that EPPC could bind to three proteins well into hydrophobic cavity, which showed good consistence with the spectroscopic measurements.Communicated by Ramaswamy H. Sarma.

The specific binding of a new 1,2,3-triazole to three blood proteins and it's appended rhodamine complex for selective detection of Hg2.

A synthesized compound, ethyl 2,5-diphenyl-2H-1,2,3-triazole-4- carboxylate (EDTC) was investigated on its physiochemical parameters and structural properties by using the quantum-chemical method. The results on the theoretical spectrum of EDTC were line with experimental fluorescence and absorption spectrum in large degree. Then EDTC was successfully synthesized to a novel rhodamine-based fluorescent probe (REDTC), which showed a distinct fluorescence enhancement upon the presence of Hg2+ in dimethyl formamide-water (DMF-H2O) buffer solution (pH 7.4). Meanwhile, the triazole appended colorless compound turns to pink upon complex formation with Hg2+ ions as 1:2 molar ratios and enables naked-eye detection. The chromogenic mechanism was determined by using spectroscopic measurements and TD DFT calculation. The fluorescence imaging experiments of Hg2+ in HeLa cell revealed that the probe REDTC could be labeled and it could be used in biological systems. Also, the intermediate EDTC was developed as a sensitive fluorescent probe for specific studies on the interactions to three kinds of blood proteins including human serum albumin (HSA), human immunoglobulin (HIg) and bovine hemoglobin (BHb) by using a series of spectroscopic methods and molecular docking under the simulative physiological conditions. The interactions between EDTC and these proteins led to the distinct fluorescence enhancement. The thermodynamic measured results further suggested that hydrophobic forces play a dominating role in stabilizing the complexes, which are in correspondence with the results from molecular docking. The UV-visible, synchronous, and three-dimensional (3D) fluorescence measurements demonstrated that EDTC influences the conformational of proteins and the microenvironment surrounding HSA, HIg, or BHb in aqueous solution.

Evolution of diffusion and structure of six n-alkanes in carbon dioxide at infinite dilution over wide temperature and pressure ranges: a molecular dynamics study.

Over wide temperature and pressure ranges, the molecular dynamics simulation is performed to study the mass transfer of six n-alkanes from n-C5H12 to n-C10H22 in CO2 at infinite dilution by calculating the diffusion coefficients, which have not yet been measured by experiment. Meanwhile, the structural properties of these systems are explored. It is found that under different temperature and pressure conditions, the variation trends of the radial distribution functions of n-alkanes are quite different, while the variation trends of the average coordination number of n-alkanes can be divided into three types. The radius of gyration and the solvent accessible surface area are both affected by temperature and carbon chain length, but their variation trends are different, and it could explain the abnormal variation trends of the radial distribution functions and the average coordination number. Graphical abstract Over wide temperature and pressure ranges, the variation trends of the average coordination number of n-alkanes can be divided into three types.

The structural properties of 5-methyl-2-phenyl-2H-1,2,3-triazole-4- carboxylic acid and chromogenic mechanism on its rhodamine B derivatives to Hg2+ ions.

5-Methyl-2-phenyl-2H-1,2,3-triazole-4-carboxylic acid (MPTC), a newly synthesized compound, was explored to study the structural properties and theoretical spectra by using GaussView5.0 program package and the time dependent density functional theory (TD DFT). The calculated quantum chemical values suggested that it is easy for MPTC to lose electron with weak electron accepting ability. And the results of experimental measurements on fluorescence and absorption spectra were consistent with that of the calculated spectra in great degree. In addition, MPTC was successfully used and synthesized a novel rhodamine B derivative RMPTC containing 1,2,3-triazole unit. It is found that there is special chromogenic response of RMPTC to Hg2+ ions in N, N-dimethylformamide (DMF)-H2O (v/v=1/1, Tris-HCl, pH7.4) with the triazole appended colorless chemosensor turned to pink and enabled naked-eye detection. The fluorescence signal for RMPTC-Hg2+ system was not affected by other coexisting metal ions. The 1:2 stoichiometric structure of RMPTC and Hg2+ is confirmed using a Job's plot estimation and TD DFT calculations. The corresponding "off-on" fluorescence mechanism of RMPTC binding to Hg2+ which were ascribed to Hg2+ inducing the ring-opened rhodamine B moiety were proposed. This study was an advancement for the application of 1,2,3-triazole compound in photophysical chemistry field and provides guidance for exploring simple and high-selectivity Hg2+ probes in aqueous solutions under physiological conditions.

MD simulation study of the diffusion and local structure of n-alkanes in liquid and supercritical methanol at infinite dilution.

The diffusion coefficients of 14 n-alkanes (ranging from methane to n-tetradecane) in liquid and supercritical methanol at infinite dilution (at a pressure of 10.5 MPa and at temperatures of 299 K and 515 K) were deduced via molecular dynamics simulations. Values for the radial distribution function, coordination number, and number of hydrogen bonds were then calculated to explore the local structure of each fluid. The flexibility of the n-alkane (as characterized by the computed dihedral distribution, end-to-end distance, and radius of gyration) was found to be a major influence and hydrogen bonding to be a minor influence on the local structure. Hydrogen bonding reduces the flexibility of the n-alkane, whereas increasing the temperature enhances its flexibility, with temperature having a greater effect than hydrogen bonding on flexibility. Graphical abstract The flexibility of the alkane is a major influence and the hydrogen bonding is a minor influence on the first solvation shell; the coordination numbers of long-chain n-alkanes in the first solvation shell are rather low.

Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture.

A combined and sequential use of quantum mechanical (QM) calculations and classical molecular dynamics (MD) simulations was made to investigate the σ and π types of hydrogen bond (HB) in benzene-water and pyrrole-water as clusters and as their liquid mixture, respectively. This paper aims at analyzing similarities and differences of these HBs resulted from QM and MD on an equal footing. Based on the optimized geometry at ωb97xD/aug-cc-pVTZ level of theory, the nature and property of σ and π types of HBs are unveiled by means of atoms in molecules (AIM), natural bond orbital (NBO) and energy decomposition analysis (EDA). In light of the above findings, MD simulation with OPLS-AA and SPC model was applied to study the liquid mixture at different temperatures. The MD results further characterize the behavior and structural properties of σ and π types HBs, which are somewhat different but reasonable for the clusters by QM. Finally, we provide a reasonable explanation for the different solubility between benzene/water and pyrrole/water.

Molecular dynamics simulation of diffusion and structure of some n-alkanes in near critical and supercritical carbon dioxide at infinite dilution.

The diffusion coefficients of n-alkanes (from CH4 to C14H30) in near critical and supercritical carbon dioxide at infinite dilution have been studied by molecular dynamics simulation. The simulation results agree well with experiment, which suggests that the simulation method is a powerful tool to obtain diffusion coefficients of solutes in fluids at high pressures. The local structures of such fluids are further investigated by calculating radial distribution functions and coordination numbers. Meanwhile, the dihedral, end-to-end distance and radius of gyration, which are calculated to characterize the flexibility of n-alkanes, are used to reasonably explain the abnormal trends on radial distribution functions and coordination numbers. Moreover, it is found that the flexibility effects on diffusion in pure n-alkanes and infinitely dilute n-alkane/CO2 system are different. The differences in MD simulation results of molecular diffusion in such systems could be qualitatively explained by the flexibility.

MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures.

Self-diffusion and structural properties of n-alkanes have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 600 K at pressures up to 300 MPa. The simulated results of lower n-alkanes are in good agreement with the existing experimental data, and support the reliability of results of the simulations of self-diffusion coefficients obtained at the extreme conditions. We predict the self-diffusion coefficients for methane, ethane, propane and n-butane at the similar reduced temperatures and pressures to draw a comparison between them. Then the correlation between self-diffusion and structural properties are further investigated by calculating the coordination numbers. Moreover, we define four distances and their corresponding relative deviations to characterize the flexibility of long-chain n-alkanes. The simulated results show that the self-diffusion of n-alkane molecules is mainly affected by the close packing, and the flexibility has a strong impact on the self-diffusion of longer n-alkane molecules.

The assessment and application of an approach to noncovalent interactions: the energy decomposition analysis (EDA) in combination with DFT of revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set.

An assessment study is presented about energy decomposition analysis (EDA) in combination with DFT including revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set. There has been little knowledge about the performance of the EDA + DFT-D3 concerning STOs. In this assessment such an approach was applied to calculate noncovalent interaction energies and their corresponding components. Complexes in S22 set were used to evaluate the performance of EDA in conjunction with four representative types of GGA-functionals of DFT-D3 (BP86-D3, BLYP-D3, PBE-D3 and SSB-D3) with three STO basis sets ranging in complexity from DZP, TZ2P to QZ4P. The results showed that the approach of EDA + BLYP-D3/TZ2P has a better performance not only in terms of calculating noncovalent interaction energy quantitatively but also in analyzing corresponding energy components qualitatively. This approach (EDA + BLYP-D3/TZ2P) was thus applied further to two representative large-system complexes including porphine dimers and fullerene aggregates to gain a better insight into binding characteristics.

One-pot preparation of thermoresponsive silica-poly(N-isopropylacrylamide) nanocomposite particles in supercritical carbon dioxide.

Inorganic/polymer nanocomposite silica-poly(N-isopropylacrylamide) (SiO(2)-PNIPA) was successfully synthesized through a one-pot approach in supercritical carbon dioxide (scCO(2)). All raw materials, N-isopropylacrylamide (NIPA), vinyltriethoxysilane (VTEO), tetraethoxysilane (TEOS), initiator 2,2'-azobisisobutyronitrile (AIBN), crosslinker N,N'-methylenebisacrylamide (MBAM) and hydrolysis agent acetic acid (AA) were introduced into one autoclave and the parallel reactions of free radical polymerization and hydrolysis/condensation occurred simultaneously in the reaction mixture with scCO(2) as solvent. The obtained novel composite particles were characterized by Fourier transform infrared spectroscopy (FTIR), scanning electronic microscopy (SEM), transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDS). The swelling ratios (SR) and lower critical solution temperatures (LCSTs) of the prepared thermoresponsive microspheres were investigated by swelling tests and ultraviolet-visible (UV) spectrophotometry, respectively. TEM images demonstrated that well-dispersed particles with diameter less than 100 nm were formed. The composite microgels exhibited higher LCSTs than poly(N-isopropylacrylamide) (PNIPA) microgels did. The in vitro release simulation of the particles in situ impregnated with ibuprofen indicated that SiO(2)-PNIPA composites could improve the drug releasing effect of the microgels as controlled drug delivery systems.