2014 Vol. 27, No. 1

Content
Content
2014, 27(1): 0-0. doi: 10.1088/1674-0068/27/1/0-0
Article
Carbon dioxide pressure-broadened ro-vibrational transitions belonging to the ?2+3?3 band of H2 16O have been measured with a sensitive cavity ring-down spectrometer. Water vapor of relatively low pressures (<0.5 Torr) was used to limit the self-collisions among water molecules. After the calibration using the precise atomic transitions of Rb and a thermo-stabilized Fabry-Pérot interferometer, 10-5 cm-1 requency accuracy has been achieved. Line parameters are derived from least-squares fitting of the spectra using the “soft” collision model. The retrieved line parameters can be applied in the study of water absorption in the CO2-rich atmospheres of planets like Venus and Mars.
The infrared absorption spectra of the CO monomer isolated in solid N2 have been recorded at various temperatures between 4.5 and 30 K. The absorption features of the fundamen-tal stretching mode show its linewidth and matrix-induced frequency shift to be weakly temperature-dependent. As the temperature of the matrix was raised, an increase in the linewidth together with a redshift in the central frequency was observed. These observa-tions were explained in terms of the quenching of the CO rotational states by the N2 matrix into closely-lying librational states. A quantitative model was then used to calculate the energy difference between these librational states. Results show that they can be thermally populated through the absorption of matrix phonons.
Different structures of graphite oxide (GO) with and without water are optimized by density functional theory. Without H2O in interlayer space, the optimized interlayer distances are about 6 ?, smaller than the experimental values of 6.5-7 ?. On the other hand, the interlayer distances of hydrated graphite oxide structures are in good agreement with experimental observations. Based on the optimized GO structures, we then simulate the immersion of GO in water or methanol by molecular dynamics. For the dry GO, water and methanol molecules do not enter the nanopore. While for the hydrated GO, the liquid molecules enter the interlayer space and enlarge the interlayer distance, semi-quantitatively reproducing theexperimental phenomena.
We perform molecular dynamics simulations for water confined between two smooth hy-drophobic walls and observe two crystalline structures with one being first reported. Both of these structures obey the ice rule. The novel ice phase is a flat hexagonal-rhombic tri-layer ice, obtained under 1 GPa load at wall separation of 1.0 nm. In this structure, the water molecules in the two layers next to one of the walls (outer layers) and in the middle layer form hexagonal rings and rhombic rings, respectively. For a molecule in the outer layers, three of its four hydrogen bonds are in the same layer, and the other one hydrogen bond connects to the middle layer. For a molecule in the middle layer, only two of its fourhydrogen-bonds are located in the same layer, and the other two connect to two different outer layers. Despite their different motifs, the area densities of the three layers are almost equal. The other structure is a flat hexagonal bilayer ice produced at wall separation of 0.8 nm under lateral pressure of 100 MPa, analogous to a system demonstrated by Koga etal. [Phys. Rev. Lett. 79, 5262 (1997)]. Both first-order and continuous phase transitions take place in these simulations.
We performed density functional theory calculations of O2, CO2, and H2O chemisorption on the UN(001) surface using the generalized gradient approximation and PW91 exchange-correlation functional at non-spin polarized level with the periodic slab model. Chemisorp-tion energies vs. molecular distance from UN(001) surface were optimized for four sym-metrical chemisorption sites. The results showed that the bridge parallel, hollow parallel and bridge hydrogen-up adsorption sites were the most stable site for O2, CO2, and H2O molecular with chemisorption energies of 14.48, 4.492, and 5.85 kJ/mol, respectively. From the point of adsorbent (the UN(001) surface), interaction of O2 with the UN(001) surface was of the maximum magnitude, then CO2 and H2O, indicating that these interactions were associated with structures of the adsorbate. O2 chemisorption caused N atoms on the surface to migrate into the bulk, however CO2 and H2O had a moderate and negligible effect on the surface, respectively. Calculated electronic density of states demonstrated the electronic charge transfer between s, p orbital in chemisorption molecular and U6d, U5f orbital.
Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against in-flammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonists. Using molecular dynamics (MD) simula-tions, we have studied the interactions between A2AAR and its agonist (adenosine), and an-alyzed the induced dynamic behaviors of the receptor. Key residues interacting with adeno-sine are identified: A632.61,I662.64, V843.32, L853.33, T883.36, F1685.29, M1775.38, L2496.51, H2506.52, and N2536.55 interacting with adenosine with affinities larger than 0.5 kcal/mol. Moreover, no interaction between adenosine and L1675.28 is observed, which supports our previous findings that L1675.28 is an antagonist specific binding reside. The dynamic be-haviors of agonist bound A2AAR are found to be different from apo-A2AAR in three typical functional switches: (i) tight “ionic lock” forms in adenosine-A2AAR, but it is in equi-librium between formation and breakage in apo-A2AAR; (ii) the “rotamer toggle switch”, T883.36/F2426.44/W2466.48, adopted different rotameric conformations in adenosine-A2AAR and apo-A2AAR; (iii) adenosine-A2AAR has a flexible intracellular loop 2 (IC2) and ɑ-helical IC3, while apo-A2AAR preferred ɑ-helical IC2 and flexible IC3. Our results indicate that agonist binding induced different conformational rearrangements of these characteristic func-tional switches in adenosine-A2AAR and apo-A2AAR.
The reagent rotational excitation effect on the stereodynamics of H+LiF→HF+Li is calcu-lated by means of the quasi-classical trajectory method on the Aguado-Paniagua2-potential energy surface (AP2-PES) constructed by Aguado et al. [J. Chem. Phys. 106, 1013 (1997)]. The angular distributions of vector correlations between products and reactants, P(?r) and P(Φr) are presented. Meanwhile, the four polarization-dependent generalized differential cross sections are computed. The results indicate that the reagent rotational quantum num-bers have impact on the vector properties of the title reaction. In addition, the reaction probability has been calculated as well.
Based on the full optimized molecular geometric structures via B3LYP/6-311+G(2d,p) method, a new gem-dinitro energetic plasticizer, bis(2,2-dinitropropyl ethylene)formal was investigated in order to search for high-performance energetic material. IR spectrum, heat of formation, and detonation performances were predicted. The bond dissociation energies and bond orders for the weakest bonds were analyzed to investigate the thermal stability of the title compound. The results show that the four N-NO2 BDEs are nearly equal to the values of 164.38 kJ/mol, which shows that the title compound is a stable compound. The detonation velocity and pressure were evaluated by using Kamlet-Jacobs equations basedon the theoretical density and condensed HOF. The crystal structure obtained by molec-ular mechanics belongs to P21 space group, with lattice parameters Z=2, a=13.8017 ?, b=13.4072 ?, c=5.5635 ?.
The excited state intramolecular proton transfer (ESIPT) coupled charge transfer of baicalein has been investigated using steady-state spectroscopic experiment and quantum chemistry calculations. The absence of the absorption peak from S1 excited state both in the experi-mental and calculated absorption spectra indicates that S1 is a dark state. The dark excited state S1 results in the very weak fluorescence of solid baicalein in the experiment. The fron-tier molecular orbital and the charge difference densities of baicalein show clearly that the S1 state is a charge-transfer state whereas the S2 state is a locally excited state. The only one stationary point on the potential energy profile of excited state suggests that the ESIPT reaction of baicalein is a barrierless process.
Molecular dynamics simulations on octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at 303-383 K and atmospheric pressure are carried out under NPT ensemble and COMPASS force field, the equilibrium structures at elevated temperatures were obtained and showed that the stacking style of molecules don't change. The coefficient of thermal expansion (CTE) values were calculated by linear fitting method. The results show that the CTE values are close to the experimental results and show anisotropy. The total energies of HMX cells with separately increasing expansion rates (100%-105%) along each crystallographic axis was calculated by periodic density functional theory method, the results of the energy change rates are anisotropic, and the correlation equations of energy change-CTE values are established. Thus the hypostasis of the anisotropy of HMX crystal's thermal expansion, the determinate molecular packing style, is elucidated.
Hydrogen evolution reaction (HER) at polycrystalline silver electrode in 0.1 mol/L HClO4 solution is investigated by cyclic voltammetry in the temperature range of 278-333 K. We found that at electrode potential φa,app decreases with φ, while pre-exponential factor A remains nearly unchanged,which conforms well the prediction from Butler-Volmer equation. In contrast, with φ nega-tive shifts from the onset potential for HER to the potential of zero charge (PZC≈-0.4 V), both Ea,app and A for HER increase (e.g., Ea,app increases from 24 kJ/mol to 32 kJ/mol). The increase in Ea,app and A with negative shift in φ from -0.25 V to PZC is explained by the increases of both internal energy change and entropy change from reactants to the transition states, which is correlated with the change in the hydrogen bond network duringHER. The positive entropy effects overcompensate the adverse effect from the increase in the activation energy, which leads to a net increase in HER current with the activation energy negative shift from the onset potential of HER to PZC. It is pointed out that entropy change may contribute greatly to the kinetics for electrode reaction which involves the transfer of electron and proton, such as HER.
We report a first-principles calculation to investigate the structural instability of rutile TiO2. The high pressure structural parameters are well reproduced. The calculated phonon disper-sion curves agree with experiments at zero pressure. Under compression, we capture a large softening around Γ point, which indicates the structural instability. From the high pressure elastic constants, we find that the rutile TiO2 is unstable when the applied pressure is larger than 17.7 GPa. Within the quasi-harmonic approximation, the thermal equation of state, thermal expansion oefficient, bulk modulus, and entropy are well reproduced. The thermal properties confirm the available experimental data and are extended to a wider pressure and temperature range.
Rotational isomerism effects on the optical spectra of a push-pull nonlinear optical chro-mophore 2-dicyanomethylen-3-cyano-4-f2-[E-(4-N,N-di(2-acetoxyethyl)-amino)-phenylene-(3,4-dibutyl)-thien-5]-E-vinylg-5,5-dimethyl-2,5-dihydrofuran (FTC) in a few solvents have been studied using the time-dependent density functional theory in combination with thepolarizable continuum model. It is shown that the maximum absorption peaks of the ro-tamers have difference of nearly 30 nm both in vacuum and in solutions. The population of the rotamers changes a lot in different solvents. Based on the geometries optimized by Hartree-Fock method, the Maxwell-Boltzmann averaged absorption has been calculated and the maximum absorption peak is in good agreement with experiment. It indicates that the bond length alternation can have an important effect on the optical spectra.
The irradiation effects of Ar+, He+, and S+ with energy from 10 eV to 180 eV on n-InP(100) surface are analyzed by X-ray photoelectron spectroscopy and low energy electron diffraction. After irradiation on the n-InP surface, damage on the surface, displacement of the Fermilevel and formation of sulfur species on S+ exposed surface are found and studied. Successive annealing is done to suppress the surface states introduced by S+ exposure. However, it is unsuccessful in removing the damage caused by noble ions. Besides, S+ ions can efficiently repair the Ar+ damaged surface, and finally form a fine 2×2 InP surface.
Graphite oxide (GO) is an important material of wide applications. Owing to its good mechanical property, the GO sheet is always expected to be stable and remains flat on various substrates. Here we demonstrate for the first time an unexpected behavior of the GO sheet on oxygen deficient ZnO film, namely the spontaneous cracking of the entire GO sheet into many small pieces. This unusual behavior has been carefully investigated by a series of control experiments and SEM, XPS and PL measurements. It is anticipated that the oxygen vacancies in the oxygen deficient ZnO film can annihilate epoxy groups of the GO sheet, resulting in the unzipping of the aligned epoxy groups on GO sheet. A prototype of the white light detector made from the cracked GO sheet is fabricated and the device demonstrates high stability and good reproducibility.
Conversion of biomass to chemicals or fuels under mild condition is still a challenge. As a platform molecule for chemicals and fuels, levulinic acid (LA) has been prepared by lique-faction of biomass at high pressure. In order to carry out the conversion from wheat straw to LA at atmosphere pressure, continuous extraction of the reactive system by an organicsolvent with a higher density than that of water was utilized for degradation of pretreated biomass. Yields of LA were measured by means of gas chromatography-mass spectrometry and nuclear magnetic resonance. The results revealed that a maximum yield of 30.66% of LA can be obtained from wheat straw. In addition, the effects of biomass pretreated conditionson the LA conversion have been studied. The study provides a new route to convert biomass to valuable chemicals at atmosphere pressure.
Three-dimensional (3D) hierarchical Co3O4 microcrystal with radial dendritic morphologies was prepared through hydrothermal reactions followed by subsequent annealing treatment. Structural and morphological characterizations were performed by X-ray diffraction, scan-ning electron microscopy and transmission electron microscopy. The gas sensing properties of the as-obtained microcrystal were investigated at 110 oC, which revealed that the 3D hierarchical porous Co3O4 microcrystal exhibited high sensitivity to ammonia, as well as a short response time of 10 s. The response characteristic indicates that the sensor has a good stability and reversibility. Detections of toxic and flammable gases, such as ethanol, acetone and benzene were also carried out at a relative low temperature. The results indicate that such hierarchical Co3O4 microcrystal would be a potential material in the field of gas sensing.
Atomistic modeling based on the density functional theory combined with the quasi-harmonic approximation is used to investigate the lattice parameters and elastic moduli of the P6 and P6' phases of Si3N4. β-Si3N4 is set as a benchmark system since accurate experiments are available. The calculated lattice constants and elastic constants of β-Si3N4 are in good agreement with the experimental data. The crystal anisotropy, mechanical stability, and brittle behavior of P6- and P6'-Si3N4 are also discussed in the pressure range of 30-55 GPa. The results show that these two polymorphs are metallic compounds. The brittleness and elastic anisotropy increase with applied pressure increasing. Besides, the phase boundariesof the β→P6'→δ transitions are also analysed. The β phase is predicted to undergo a phase transition to the P6' phase at 40.0 GPa and 300 K. Upon further compression, the P6'→δ transition can be observed at 53.2 GPa. The thermal and pressure effects on the heat capacity, cell volume and bulk modulus are also determined. Some interesting features are found at high temperatures.
The excited state photophysics of low bandgap polymer APFO3 has been investigated in detail. The chemical calculations confirm that the intrachain charge transfer (ICT) may occur after photo-excitation and is mainly responsible for the first absorption band. The transient absorption results confirm that ICT indeed exists and competes with the vibra-tional relaxation at the same time, when APFO3 is in a monodisperse system. This ICT process would disappear due to the influence of interchain interaction when APFO3 is in the condensed phase, where the exciton decay would be dominant in the relaxation process after photoexcitation. The photoexcitation dynamics of APFO3 film blending with PC61BM are presented, which shows that the exciton may be dissociated completely as the percentage of PC61BM reaches ~50%. Meanwhile, the photovoltaic performance based on blend het-erojunction shows that the increase of photocurrent is little if the percentage of PC61BM exceeds ~50%. Overall, the present study has covered several fundamental processes taking place in the APFO3 polymer.
DNA and histone protein are important in the formation of nucleosomal arrays, which are the first packaging level of DNA into a more compact chromatin structure. To characterize the interactions of DNA and histone proteins, we reconstitute nucleosomes using lambda DNA and whole histone proteins by dialysis and perform direct atomic force microscopy (AFM) imaging. Compared with non-specific DNA and histone binding, nucleosomes are formed within the assembled “beads-on-a-string” nucleosomal array by dialysis. These observations facilitate the establishment of the molecular mechanisms of nucleosome and demonstrate the capability of AFM for protein-DNA interaction analysis.
One-dimensional alumina photonic crystals with defect modes were successfully fabricated through inserting a constant voltage waveform into the periodic voltage signals. The trans-mission spectra show that the thickness of defects plays a key role in determining the trans-mittance of defect modes. When the thickness was ?180 nm, an obvious defect mode withthe high transmittance of 55% and a narrow full width at half maximum of 18 nm was observed in the original photonic band gaps. The defect mode shifted linearly with the increasing of refractive index of the analytes infiltrated into pores, indicating its potential application in chemical sensing or bio-sensing.
Chinese abstract