2009 Vol. 22, No. 3

Article
Content
2009, 22(3)
Molecular dynamics simulations with embedded atom method potential were carried out for Al nanoparticles of 561 atoms in three structures: icosahedron, decahedron, and truncated octahedron. The total potential energy and specfic heat capacity were calculated to estimate the melting temperatures. The melting point is 540±10 K for the icosahedral structure,500±10 K for the decahedral structure, and 520±10 K for the truncated octahedral structure.With the results of mean square displacement, the bond order parameters and radius of gyration are consistent with the variation of total potential energy and specific heat capacity. The relaxation time and stretching parameters in the Kohlraush-William-Watts relaxation law were obtained by fitting the mean square displacement. The results show that the relationship between the relaxation time and the temperatures is in agreement with standard Arrhenius relation in the high temperature range.
When the molecular ions XYZ+(XY2+) are excited simultaneously from an electronic state E0 into two higher electronic states Eα and Eβ with supervened dissociation or predissociation, competition between the α and β excitation-dissociation channels occurs. A theoretical model is provided to deal with the competition of the two excitation-dissociation channels with more than two kinds of ionic products for XYZ+ (XY2+). Supposing that the photo-excitation rates of two states Eα and Eβare much less than their dissociation or pre-dissociation rates, a theoretical equation can be deduced to fit the measured data, which reflects the dependence of the product branching ratios on the intensity ratios of two excitation lasers. From the fitted parameters the excitation cross section ratios are obtained. In experiment, we studied the competition between two excitation-dissociation channels of CO2+. By measuring the dependence of the product branching ratio on the intensity ratio of two dissociation lasers and fitting the experiment data with the theoretical equation, excitation cross section ratios were deduced.
The dynamics of molecular rotational wave packets of D2 induced by ultrashort laser pulses was investigated numerically by solving the time-dependent Schrödinger equation. Results show that an ultrashort pulse can manipulate a coherent rotational wave packet of D2 selectively. In the calculation, a first laser pulse was used to create a coherent rotational wave packet from an initial thermal ensemble of D2 at the temperature of 300 K. The second laser pulse was used to manipulate the rotational wave packet selectively around the first quarter and the three quarters revival. The alignment parameter and its Fourier transform amplitude both illustrate that the relative populations of even and odd rotational states in the final rotational wave packet of D2 can be manipulated by precisely selecting the time delay between the first and the second ultrashort pulse.
Quantum chemical calculations were used to estimate the bond dissociation energies (BDEs) for 13 substituted chlorobenzene compounds. These compounds were studied by the hybrid density functional theory (B3LYP, B3PW91, B3P86) methods together with 6-31G**and 6-311G** basis sets. The results show that B3P86/6-311G** method is the best method to compute the reliable BDEs for substituted chlorobenzene compounds which contain the C-Cl bond. It is found that the C-Cl BDE depends strongly on the computational method and the basis sets used. Substituent effect on the C-Cl BDE of substituted chlorobenzene compounds is further discussed. It is noted that the effects of substitution on the C-Cl BDE of substituted chlorobenzene compounds are very insignificant. The energy gaps between the HOMO and LUMO of studied compounds are also investigated and from this data we estimate the relative thermal stability ordering of substituted chlorobenzene compounds.
The influence of Li intercalation on the electronic structures of oxygen and vanadium ions in α-V2O5 was investigated using first-principles calculations based on the density functional theory with local density approximation. Two different intercalation sites for Li in the V2O5 lattices were considered. The calculation results demonstrate that intercalated Li ions at different sites show different effects on the electronic structures of O2p and V3d orbitals. But in both cases Li intercalation will weaken the V=O1 bonding and cause the split-off in V3d valence band to narrow or even disappear and simultaneously broaden the O2p conduction band. Further, the average electron transfer number from per intercalated Li2s to V3d orbitals is determined to total be about 0.52.
The Weakest Bound Electron Potential Model theory is used to calculate transition probability-values and oscillator strength-values for individual lines of Sc(III) and Y(III).In this method, by solving the Schr?dinger equation of the weakest bound electron, the expressions of energy eigenvalue and the radial function can be obtained. And a coupled equation is used to determine the parameters which are needed in the calculations. The obtained results of Sc(III) from this work agree very well with the accepted values taken from the National Institute of Standards and Technoligy (NIST) data base, most deviations are within the accepted level. For Y(III) there are no accepted values reported by the NIST data base. So we compared our results of Y(III) with other theoretical results, good agreement is also obtained.
On the basis of information theory and statistical methods, we use mutual information, n-tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes.The magnitude distribution of the long range correlation which can be reflected by the mutual information is P5>P5a>P5b (P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uncorrelated sequences in human Y chromosome palindrome 5, respectively); and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is P5>P5a>P5b>random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uncorrelated sequence, the long range and short range correlation decrease gradually. However, the random uncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.
According to experimental data available for the complex refractive index of particular dielectrics, a dielectric spectrum formula is proposed by the least square fitting technique combined with selected natural frequencies. From the dielectric spectrum formula, the spectra of optical and dielectric constants can be obtained in the whole frequency region. Three dielectrics, water, ethanol, and toluene, are taken as examples.In the region where the experimental data are available, the spectra of the optical constants calculated by the formula are in good agreement with the real refractive spectrum obtained by Kramers-Kronig (K-K) transform and the experimental imaginary refractive spectrum. In the region where no experimental data are available, the extrapolation of our formula can make predictions. The merits of the present treatment are that we are able to get the uniform spectrum formula, without splitting into different frequency sections, and the analytical form of the dielectric spectra will be useful in the theoretical description of solvation dynamics
Three methods including the atomic resolved density of state, charge difference density, and the transition density matrix are used to visualize metal to ligand charge transfer (MLCT) in ruthenium(II) ammine complex. The atomic resolved density of state shows that there is density of Ru on the HOMOs. All the density is localized on the ammine, which reveals that the excited electrons in the Ru complex are delocalized over the ammine ligand. The charge difference density shows that all the holes are localized on the Ru and the electrons on the ammine. The localization explains the MLCT on excitation. The transition density matrix shows that there is electron-hole coherence between Ru and ammine. These methods are also used to examine the MLCT in Os(bpy)2(p0p)Cl (“Osp0p”; bpy=2,2’-bipyridyl; p0p=4,4’-bipyridyl) and the ligand-to-ligand charge transfer (LLCT) in Alq3. The calculated results show that these methods are powerful to examine MLCT and LLCT in the metal-ligand system.
The title compound glaucocalyxin A (1) (7α,14β-dihydroxy-ent-kaur-16-en-3,15-dione) isolated from the leaves of isodon excisoides was characterized by IR, 1H NMR, 13C NMR,1H-1H COSY, HMQC, HMBC, and EIMS, and its crystal structure was determined by singlecrystal X-ray diffraction. The X-ray crystal structure revealed that the molecular backbone of the chosen crystal is a tetracyclic system, including three six-membered rings and a five-membered ring, and the three six-membered rings are in a chair-like conformation. The five-membered ring adopts a twisted envelope-like conformation, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. The molecules form extensive networks through the intra- and intermolecular hydrogen bonds.The experimental NMR data were interpreted with the aid of magnetic shielding constant calculations, by means of the GIAO (gauge-lncluding atomic orbitals) method. Calculated and experimental results were compared with a satisfactory level of agreement. Molecular electrostatic potential map was used in an attempt to identify key features of the diterpenoid glaucocalyxin A that is necessary for its activity. Calculations of molecular electrostatic potential and stabilization energies suggest that the protonation of glaucocalyxin A will be able to occur on carbonyl oxygen atoms.
A three-dimensional quantitative structure-activity relationship (3D-QSAR) study of a series of 7,8-dialkyl-1,3-diaminopyrrolo-[3,2-f] quinazolines with anticancer activity as dihydrofolate reductase (DHFR) inhibitors was carried out by using the comparative molecular field analysis (CoMFA), on the basis of our reported 2D-QSAR of these compounds. The established 3D-QSAR model has good quality of statistics and good prediction ability; the non cross-validation correlation coefficient and the cross-validation value of this model are 0.993 and 0.619, respectively, the F value is 193.4, and the standard deviation SD is 0.208.This model indicates that the steric field factor plays a much more important role than the electrostatic one, in satisfying agreement with the published 2D-QSAR model. However,the 3D-QSAR model offers visual images of the steric field and the electrostatic field. The 3D-QSAR study further suggests the following: to improve the activity, the substituent R’ should be selected to be a group with an adaptive bulk like Et or i-Pr, and the substituent R should be selected to be a larger alkyl. In particular, based on our present 3D-QSAR as well as the published 2D-QSAR, the experimentally-proposed hydrophobic binding mechanism on the receptor-binding site of the DHFR can be further explained in theory. Therefore, the QSAR studies help to further understand the “hydrophobic binding”action mechanism of this kind of compounds, and to direct the molecular design of new drugs with higher activity.
Ignition timing control is of great importance in homogeneous charge compression ignition engines. The effect of hydrogen addition on methane combustion was investigated using a CHEMKIN multi-zone model. Results show that hydrogen addition advances ignition timing and enhances peak pressure and temperature. A brief analysis of chemical kinetics of methane blending hydrogen is also performed in order to investigate the scope of its application, and the analysis suggests that OH radical plays an important role in the oxidation.Hydrogen addition increases NOx while decreasing HC and CO emissions. Exhaust gas recirculation (EGR) also advances ignition timing; however, its effects on emissions are generally the opposite. By adjusting the hydrogen addition and EGR rate, the ignition timing can be regulated with a low emission level. Investigation into zones suggests that NOx is mostly formed in core zones while HC and CO mostly originate in the crevice and the quench layer.
The reaction of Nb+ with CS2, producing cationic transition-metal sulfide and CS, was taken as a representative example to elucidate the overall mechanism of reactions of second-row early transition metal ions with CS2. The reactions in both triplet and quintet state were studied by using the UB3LYP density functional method with the Stuttgart pseudo potentials and corresponding basis sets for Nb+ and the standard 6-311+G(2d) basis sets for C and S. The geometries for reactants, the transition states, and the products were completely optimized. All the transition states were verified by vibrational analysis and intrinsic reaction coordinate calculations. The results show that the reaction mechanism between niobium ion and CS2 is an insertion-elimination mechanism. Intersystem crossing may occur in the reaction Nb+ with CS2 and a minimum energy crossing point was found.
The non-additivity of the methyl groups in the single-electron lithium bond was investigated using ab initio calculations at the B3LYP/6-311++G** and UMP2/6-311++G** levels.The strength of the interaction in the H3C…… LiH, H3CH2C……LiH, (H3C)2HC…… LiH, and (H3C)3C…… LiH complexes was analyzed in term of the geometries, energies, frequency shifts,stabilization energies, charges, and topological parameters. It is shown that (H3C)3C radical with LiH forms the strongest single-electron lithium bond, followed by (H3C)2HC radical,then H3CH2C radical, and H3C radical forms the weakest single-electron lithium bond. A positive non-additivity is present among methyl groups. Natural bond orbital and atoms in molecules analyses were used to estimate such conclusions. Furthermore, there are few linear/nonlinear relationships in the system and the interaction mode of single-electron Li-bond is different from the single-electron H-bond and single-electron halogen bond.
The shell-model molecular dynamics method was applied to simulate the melting temperatures of SrF2 and BaF2 at elevated temperatures and high pressures. The same method was used to calculate the equations of state for SrF2 and BaF2 over the pressure range of 0.1 MPa-3 GPa and 0.1 MPa-7 GPa. Compared with previous results for equations of state,the maximum errors are 0.3% and 2.2%, respectively. Considering the pre-melting in the fluorite-type crystals, we made the necessary corrections for the simulated melting temperatures of SrF2 and BaF2. Consequently, the melting temperatures of SrF2 and BaF2 were obtained for high pressures. The melting temperatures of SrF2 and BaF2 that were obtained by the simulation are in good agreement with available experimental data.
A combination of X-ray powder diffraction, thermogravimetric analysis, diffuse reflection infrared Fourier transform, and 31P magic-angle spinning nuclear magnetic resonance techniques with density function computation was used to elucidate the products and mechanism of the reactions among silica, H3PO4, and NaH2PO4during the preparation of silica supported H3PO4and NaH2PO4catalysts. The spectral test results indicate that besides polyphosphoric acid, silicon phosphates on silica supported H3PO4 are also formed. On silica supported NaH2PO4 only sodium polyphosphates are present. Density functional theory (DFT) simulations indicate that in the initial stage, reaction of H3PO4 with silanol groups on the silica support is more favorable than that between H3PO4 itself. In contrast, dimerization and trimerization of NaH2PO4 are predicted to be the predominant initial reactions for the silica supported NaH2PO4catalyst.
Sulfated zirconia-lanthana (SO42-/ZrO2-La2O3) precursors were prepared by ultrasonic co-precipitation method and followed by aging at different temperature. The precursors weretreated by 0.5 mol/L H2SO4. Samples of SO42-/ZrO2-La2O3nano-crystalline catalysts wereobtained by baking the treated precursors at different temperatures. The acidic properties ofSO42-/ZrO2-La2O3 were tested by the Hammett indicator method. The phase composition,specific area, particle structure, and surface state were characterized by X-ray diffraction,BET, transmission electron microscopy, infrared spectrum, and X-ray photoelectron spec-troscopy. The catalytic activities were estimated by esterification of acetic acid with glycerin.It was shown that the catalyst prepared by ultrasonic stirring and low temperature (-15 ºC)exhibited highly active sites and high catalytic property.
Manganese oxide hollow spheres were prepared by a novel and facile approach using pH-responsive microgels as templates. The final products were thoroughly characterized with X-ray powder diffraction, thermogravimetric analysis, scanning electron microscopy, Fourier transform infrared, and transmission electron microscopy. The results reveal that the shell thickness of manganese oxide hollow spheres increased with the dosage of KMnO4, which implies that a controllable and feasible strategy for manganese oxide hollow spheres prepa-ration has been established. Further studies on the microgels template showed some of them had an irreversible swelling/deswelling transition due to the uneven cross-link extent. Based on the results, a probable formation mechanism for the hollow spheres was proposed.
Using the same conditions and various starting materials, such as lead acetate trihydrate, tetrabulyl titanate, zirconium n-butoxide, and acetylacetone, two kinds of solid precursors, lead zirconate titanate (PZT, Zr/Ti=15/85) and lead titanate (PT), were fabricated. With three different combinations, namely, PZT, PT/PZT-PZT/PT, and PT/PZT/-/PZT/PT, three multilayer thin films were deposited on three Pt-Ti-Si3N4-SiO2-Si substrates by a modified solgel process. The fabrication process of the thin films is discussed in detail.We found that there is a large built-in stress in the thin film, which can be diminished by annealing at 600 ºC, when the gel is turned into solid material through drying and sintering.The Raman scattering spectra of the films with different compositions and structures were investigated. With the help of X-ray diffraction (XRD) analyzer and Raman scattering spectra analyzer, it was found that the thin films with the PT/PZT-PZT/PT structure have reasonable crystallinity and less residual stress. XRD testing shows that the diffraction pattern of the multilayer film results from the superimposition of the PZT and PT patterns.This leads to the conclusion that the PT/PZT-PZT/PT multilayer thin film has a promising future in pyroelectric infrared detectors with high performance.