2009 Vol. 22, No. 5

Editorial
Article
The fast phase-transitional process of ploy(N-isopropylacrylamide) (PNIPAM) in deuterated solution was studied by laser induced temperature jump technique combined with time-resolved mid-infrared absorbance difference spectroscopy on nanosecond level. The multi-peaks of amide I0 band of PNIPAM among the energy range of 1565-1700 cm-1 was experimentally resolved to three groups (i, ii, iii) for the first time, while the distinct three-stage procedure in the phase transitional process of long-chain PNIPAM was observed firstly too. Furthermore, proper assignments were also made for the three group peaks in amide I′band and the three steps in the kinetics process of long-chain PNIPAM.
Phase behaviors of different binary systems involving 1-dodecyl-3-methylimidazolium chlo-ride ([C12mim]Cl) and H2O, [C12mim]Cl and different alcohols (1-butanol, 1-pentanol, 1-hexanol and 1-octanol) are investigated at 25 °C. Hexagonal liquid crystal phase (H1) is identified in [C12mim]Cl/H2O system, and lamellar liquid-crystalline (Lα) phase is found in [C12mim]Cl/alcohols systems by using polarized optical microscopy and small-angle X-ray scattering techniques. The formation of such phases is considered as a synergetic result of the solvatophobic force and the hydrogen-bonded network comprising an imidazolium ring,chloride ion and water (or alcohols), which can be confirmed by Fourier transform infrared spectra. It is noticeable that in [C12mim]Cl/1-octanol system, the lattice spacings of lamel-lar phase increase with increasing C12mimCl concentration, which is opposite to the results of [C12mim]Cl/H2O system. This may result mainly from stronger static repulsion among hydrophilic headgroups of imidazolium salts arranged in the bilayers of lamellar structures.Further measurements by diffrential scanning calorimetry indicate that the lamellar phase is stable within a wide temperature range above room temperature. However, the latticespacings decrease with the increase of temperature, which may be due to the softening of the hydrocarbon chain of [C12mim]Cl molecules. In different alcohols systems, it is foundthat the lamellar lyotropic liquid crystal structure is easier to be formed when the carbon chain length becomes longer.
The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate (NaBF4)/water mixture at room temperatures were studied with molec-ular dynamics simulation. Different concentrations of water (6.25%, 25.0%, 50.0%, 75.0%,90.0%, and 99.6%) in NaBF4/water mixture were simulated to understand the structureand dynamics. It was shown that water molecules tend to be isolated from each other inmixtures with more ions than water molecules in both liquids. With increase of the molarfraction of water in the mixture, the rotation bands and the bending bands of water displayred shift whereas the O-H stretch bands show blue shift, and the decay of the reorientationcorrelation function becomes slower. This suggests that the molecules are hindered and theirmotions are difficult and slow, due to the hydrogen-bond interactions and the inharmonicinteractions between the inter- or intra-molecular modes.
The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5.The radius of gyration (Rg), subunit interactions, and residue flexibility were analyzed.The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loop-helix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces.The Rg of catalytic domain at 360 K shows 0.16 ? higher than that at 300 K,but Rg of small C-terminal domain has no obvious difference.The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction.Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI.This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously.Our results reveal the relationship between temperature and structure flexibility of TtXI,and play an important role in understanding the thermostability of thermophile protein with multiple subunits.
Three-dimensional quantitative structure activity relationship (3D-QSAR) and docking stud-ies of a series of arylthioindole derivatives as tubulin inhibitors against human breast cancer cell line MCF-7 have been carried out. An optimal 3D-QSAR model from the compar-ative molecular field analysis (CoMFA) for training set with significant statistical quality (R2=0.898) and predictive ability (q2=0.654) was established.The same model was further applied to predict pIC50 values of the compounds in test set,and the resulting predictive correlation coefficient R2(pred) reaches 0.816,further showing that this CoMFA model has high predictive ability. Moreover, the appropriate binding orientations and conformations of these compounds interacting with tubulin are located by docking study, and it is very in-teresting to find the consistency between the CoMFA field distribution and the 3D topology structure of active site of tubulin. Based on CoMFA along with docking results, some impor-tant factors improving the activities of these compounds were discussed in detail and were summarized as follows: the substituents R3-R5 (on the phenyl ring) with higher electroneg-ativity, the substituent R6 with higher electropositivity and bigger bulk, the substituent R7 with smaller bulk, and so on. In addition, five new compounds with higher activities have been designed. Such results can offer useful theoretical references for experimental works.
A generalized response function based on the use of dielectric spectra for dielectric relaxationprocess is derived.We apply the general response function to the special case in order to examine how special dielectric relaxation functions developed by other authors for solvent relaxation can be derived based on our formulations.Three typical solvents,water,methanol,and acetonitrile are used to investigate the electronic polarization processes of polar solvents.The solvent electronic polarization process is shown after a linear variation with the external electric field imposed on the solvent.The results show a conclusion that the electronic polarization of the solvents will accompany the electronic transition synchronously, without time lag.
The geometries,electronic structures,polarizabilities and hyperpolarizabilities,as well as the UV-Vis spectra of the two organic dye sensitizers containing bis-dimethylfluorenyl amino benzofuran were studied via density functional theory (DFT) and time-dependent DFT.The features of electronic absorption spectra were assigned on account of the agreement between the experiment and the calculations.The absorption bands in visible region are related to photoinduced electron transfer processes, and the dimethylfluorenyl amino benzo[b]furan groups are major chromophore thatcontributed to the sensitization of photo-to-current conversion.The role of vinylene group in geometry,electronic structure and spectra property is analyzed according to the comparative study of the dyes.
We adopt the density function theory with generalized approximation by the Beeke exchange plus Lee-Yang-Parr correlation functional to calculate the electronic first-principles band structure of tin-phthalocyanine (SnPc).The intermolecular interaction related to transport behavior was analyzed from the ?-point wave function as well as from the bandwidths and band gaps.From the calculated bandwidths of the frontier bands as well as the effective masses of the electron and hole, it can be concluded that the mobility of the electron is about two times larger than that of the hole.Furthermore, when several bands near the Fermi surface are taken into account, we find that the interband gaps within the unoccupied bands are generally smaller than those of the occupied bands, indicating that the electron can hop from one band to another which is much easier than the hole. This may happen throughelectron-phonon coupling for instance, thus effectively yielding an even larger mobility for theelectron than for the hole. These facts indicate that in SnPc the electrons are the dominant carriers in transport, in contrast to most organic materials.
The stochastic simulation algorithm (SSA) accurately depicts spatially homogeneous well-stirred chemically reacting systems with small populations of chemical species and properly represents noise, but it is often abandoned when modeling larger systems because of its computational complexity.In this work,a twin support vector regression based stochastic simulations algorithm (TS3A) is proposed by combining the twin support vector regression and SSA,the former is a well-known robust regression method in machine learning.Numeri-cal results indicate that this proposed algorithm can be applied to a wide range of chemically reacting systems and obtain significant improvements on effciency and accuracy with fewer simulating runs over the existing methods.
The interactions and structures of the urea-water system are studied by an all-atom molec-ular dynamics (MD) simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulations. The structures of urea-water mixtures can be classified into different regions from the analysis of the hydrogen-bonding network. The urea molecule shows the certain tendency to the self-aggregate with the mole fraction of urea increasing.Moreover,the results of the MD simulations are also compare with the chemical shifts and viscosities of the urea aqueous solutions, and the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data such as chemical shifts of the hydrogen atom and viscosity.
The hydrogen bonding character between the BF4- and glycine was theoretically studied at the level of B3LYP/6-31+G*,single point energies were performed at the level of B3LYP/6-311++G**.The relevant geometrical characteristics, energy properties, as well as the characters of the intramolecular hydrogen bonds have been studied.Atoms in molecule theory topological analysis indicated the (3,-1) critical points for hydrogen bonds.In addition,the electron density and Laplacian were in the range suggested for the hydrogen bonds.Especially, the changes of atomic charge, dipole moment, energy as well as volume of the hydrogen upon hydrogen bonds formation were systemitically discussed.
Theoretical studies of the dynamics of the reactions O(3P)+H2/HD(v=0, j=0)→OH+H have been performed with quasi-classical trajectory method (QCT) on an ab initio potential surface for the lowest triplet electronic state of H2O(3A" ). The QCT-calculated integral cross sections are in good agreement with the earlier time-dependent quantum mechanics results. The state-resolved rotational distributions reveal that the product OH rotational distributions for O+HD have a preference for populating highly internally excited states compared with the O+H2 reaction. Distributions of differential cross sections show that directions of scattering are strongly dependent on the choice of quantum state. The polar-ization dependent generalized differential cross-sections and the distributions were calculated and a pronounced isotopic effect is revealed. The calculated results indicate that the product polarization is very sensitive to the mass factor.
The developed visualization methods of two dimensional (2D) site and three dimensional (3D) cube representations have been performed to show the orientation of transition dipole,charge transfer,and electron-hole coherence in two-photon absorption (TPA).The 3D cube representations of transition density can reveal visually the orientation and strength of tran-sition dipole moment,and charge different density show the orientation of charge transfer in TPA.The 2D site representation can reveal visually the electron-hole coherence in TPA.The combination of 2D site and 3D cube representations provide clearly inspect into the charge transfer process and the contribution of excited molecular segments for TPA.
The fabrication of magnetorheological (MR) elastomers was studied by two vulcanization methods, including heat vulcanization (HV) and radiation vulcanization (RV), were em-ployed to fabricate MRE samples. The dynamical mechanical properties were characterized by using a dynamic mechanic analyzer. In particular, both the MR effect and its durability were investigated.The experimental results showed that RV samples have large magneto-induced modulus,large zero-field modulus,and good durability property of MR effect.To explain these results,cubic deformation and plasticizer migration were analyzed. Large magneto-induced modulus of RV sample results from cubic deformation during vulcaniza-tion process. And the plasticizer migration results in better durability of MR effect.
PVP/SDS complex was applied as a probe to study the interaction between β-cyclodextrin(β-CD) and sodium dodecyl sulfate (SDS) in aqueous solution. It has been found thata critical concentration, namely cs, exists in the relative viscosity of solution containingPVP/SDS complex versus β-CD concentration plot. As the β-CD concentration is lessthan cs, the relative viscosity of solution decreases sharply by adding β-CD into solution successively. On the other hand, as the β-CD concentration is greater than cs, the relative viscosity of solution increases gradually by adding β-CD into solution. The decrease of the relative viscosity of solution containing PVP/SDS in the presence of β-CD is just due to the inclusion complex of β-CD with the guest molecule SDS. And, this inclusion interaction takes down SDS from the PVP chains in solution. The ratio of the host molecule β-CD to the guest molecule SDS can be calculated from cs. In our experiment the inclusion ratio of β-CD to SDS is 1/1. The further experimental results indicate that cs is associated with SDS but free from PVP in PVP/SDS complex. However, the inclusion ratio of β-CD to SDS has proved to be independent of either SDS or PVP in PVP/SDS complex.
Magnetorheological elastomer (MRE) is a new kind of smart materials, the rheological prop-erties can be controlled rapidly by the external magnetic field. It is mainly composed of rubber and micron-sized ferromagnetic particles, which forms a chain-like structure. There-fore its mechanical, electric, and magnetic properties can be changed by the applied magnetic field, which is called as the magneto-induced effect. But this effect is not remarkable enough currently for the engineering application. So it is important for material preparation to op-timize parameters to enhance the magneto-induced effect. In this work, based on chain-like model, some factors influencing the magneto-induced effect of MRE were analyzed theo-retically by using dipole method with the normal distribution of chain's angle introduced.The factors included the oblique angle of particles chains, magnetic field intensity, and shear strain, etc. Some experiments were also carried out.