MONTE CARLO SIMULATION ON AQUEOUS SOLUTION OF BIOLOGICAL MOLECULES——ALANINE SOLUTION

The Monte Carlo simulation is performed for a cluster consisting of a neutral alanine molecule surrounded by 56 water molecules. The average water-water and alanine-water interaction energies are found. The space surrounding the alanine molecule is divided into three regions, where the central atoms are C' atom for the earboxyl group region, N atom for the amino group region and C~β atom for the methyl group region. The water-water and water-alanine interaction energies as functions of the distance between the oxygen atom in a water molecule and the central atom in each region are calculated. In each region the orientational correlation function for the dipole moments of water molecules, the radial distribution function for the oxygen and hydrogen atoms of water molecules are evaluated. In addition, the numbers of water molecules in the first solvation shells of each region and of entire alanine molecule are also counted.     

A partially projected wave function for radicals

A partially projected wave function for odd electron systems with quantum number M=1/2, containing μu spin functions α and μ spin functions α, with fractional spin component αS_z=1/2 and 3/2 are derived from the totally projected wave function. To obtain these wave functions new symmetry relations between Sanibel coefficients for the odd electron case have been found, as well as the relations between primitive spin functions and their spin permutations. The wave function for the doublet state is shown not to contain contamination of the quadruplet state, and the wave function for the quadruplet does not have contamination of the duplet. Both wave functions exhibit equal forms except in the signs of their summation terms. The number of primitive spin functions depends on the number of electrons (n_s), it grows linearly as n_s=(N+3)/2. It can be considered as a generalization of the half projected Hartree–Fock wave function to the odd electron case. The HPHF wave function is defined for even electron systems and consists of only two Slater determinants, it has been shown to introduce some correlation effects and it has been successfully applied to calculate the low-lying excited states of molecules. Therefore, this investigation is the first step to propose a method to calculate the excited states of radicals when other methods are impracticable. This revised version was published online in July 2006 with corrections to the Cover Date.     

Ab initio VB Studies of the Ground and Low-lying Excited States of BeH and BH

A scheme has been proposed to classify valence bond(VB) wave functions for the calculations of ground and excited states,according to the symmetry properties of one-electron orbitals which are involved in the construction of VB wave functions.This scheme is illustrated by the examples of BeH and BH.Ab initio VB computations of these two test molecules in combination with the present classification scheme give reliable results.For example,calculation results show that the state C2∑ of BeH is stable,with the bonding energy 0.87 eV and bond length 0.238nm,which are in good agreement with those obtained by Gerratt et al.The bonding features of ground and low-lying excited states of BeH and BH are discussed.     

胶溶-水热晶化过程中纳米TiO2相稳定性研究

The phase stability of nanocrystaline anatase and rutile TiO2 in sols peptized at different temperature has been studied by X-ray Diffraction (XRD) and thermodynamical analysis. The results show that the stability of nanocrystaline TiO2 of different crystal types is a function of particle size. According to the thermodynamical analysis, anatase TiO2 becomes more stable than rutile TiO2 when the particle size is less than ca. 14 nm, which coincides with the experimental data obtained by XRD. Both surface Gibbs free energy and surface stress play important roles in the thermodynamically phase stability. Comparing the data calculated thermodynamically with the experimental results obtained under different temperatures, it is found that the constant K in the function relation, f=KGS, between surface free energy GS and surface stress f is temperature dependent and equal to 1 at 333 K and 2 at 453 K, respectively.     

The caged state of some small molecules in the C_(60) cage

The potential energy curves of some small molecules, H2, N2, O2, F2, HF, CO and NO, in the caged state within C60 cage and in the free state have been calculated by the quantum-chemical method AM1. In this study, the focus is on the cage effect of C60, and the concept of caged state is put forward. The results show that the bond lengths in the caged states are not much different from those in their corresponding free states, but the bond intensities in the caged states are much greater than those in their corresponding free states.     

Theoretical Investigation on the Relationship between the Structures and Antioxidant Activities of Myricetin and Dihydromyricetin

The geometry of myricetin and dihydromyricetin was optimized by DMol3 program based on DFT. The optimized structures have been proved to be stable by real frequencies obtained.The parameters of geometry optimization,vibration frequencies,atomic charges,thermodynamics,Fukui functions,and frontier molecular orbital had been obtained. The thermodynamic properties of 2 molecules were fitted and the relationship between the thermodynamic function and temperature was obtained. The correlation coefficient of the obtained equations is larger than 0.99,indicating that the function is approximately linear in the whole temperature range. The calculated results showed the O–H molecular structures were the main group affecting the antioxidant activity and the oxygen in the benzene ring is the electrophilic reaction site. Ortho-OH on the benzene formed intramolecular hydrogen bonds,which contributed to the stability of the benzene ring. It may be the active site for the occurrence of the reaction.     

Electronic factor in electron self-exchange reaction of hydrated redox ion pairs from thermodynamic data

An accurate scheme for determining the electronic factor of the electron self-exchange reaction in solution is presented in this paper. The used various activation parameters and slopes of potential energy surfaces are obtained in terms of an improved activation model and the accurate potential function determined from the vibrational spectroscopic and thermodynamic data. The coupling matrix elements are determined using numerical integral method over the perturbed double-zeta Slater-type state functions. Theoretical results of electronic factor in this work are found in close agreement with those extracted from experimental rate constant data and to be less than unity. Results indicate that outer-sphere electron transfer reactions in solution involving hydrated transition metal ions are nonadiabatic in nature.     

Prediction of the Frontier Electronic States in a Finite Single-wall Carbon Nanotube

A theoretical model is summarized into the shorter vector principle. It is used to predict the topological structure of wave function and the oscillation rule of energy gap in various types of finite carbon nanotubes (CNTs). The theoretical model indicates that the characteristics of the electronic states only depend on the nanotube size and its symmetry along the shorter vector direction. In this direction, the wave functions of the original 3m (or 3m/2) periodicity are also suitable for armchair, chiral and zigzag finite CNTs with the C2 (Cs), C1 and Cn point groups, respectively. Energy gaps present the oscillation with 3m (or 3m/2) or odd-even n. The first principle calculations for some prototype systems are performed. The results are consistent with the theoretical model.     

Frist-principles Band Structures Calculation of Tin-phthalocyanine

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 F-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 through electron-phonon coupling for instance, thus effectively yielding an even larger mobility for the electron than for the hole. These facts indicate that in SnPc the electrons are the dominant carriers in transport, in contrast to most organic materials.     

COMPUTERIZED SIMULATION OF MOLTEN LiFKCl SOLUTION BY MONTE CARLO METHOD——RADIAL DISTRIBUTION FUNCTION AND THERMODYNAMIC PROPERTIES

The structure of molten LiF-KCl solution has been simulated by Monte Carlo method.The partial radial distribution function of ions,the molar volume,enthalpy and the heat of mixing of LiF-KCl melt have been calculated. Some results of calculation agree with experimental data.The results of calculation indicate that the average distance between Li~+ and F~- ions decreases significantly after the mixing of molten LiF with KCl, and the free volume distribution of the LiF-KCl melt is far from uniform.     

Understanding the interactions between tris(pentafluoroethyl)-trifluorophosphate-based ionic liquid and small molecules from molecular dynamics simulation

Tris(pentafluoroethyl)trifluorophosphate ([FEP])-based ionic liquids have been widely applied in many fields. For better understanding the properties of [FEP]-based ionic liquids, the interactions between 1-hexyl-3-methylimidazolium ([hmim])[FEP] and small molecules were investigated by molecular dynamics simulations in this work. The small molecules are water, methanol and dimethyl ether. The united-atom (UA) force fields were proposed for methanol and dimethyl ether based on AMBER force field. The densities, enthalpies of vaporization, excess molar properties, and diffusion coefficients of the mixtures were calculated, as well as the microscopic structures characterized by radial distribution functions. Both of the results of the excess energies and microscopic properties show that the strongest interaction is between [hmim][FEP] and dimethyl ether, whereas the interaction between [hmim][FEP] and water is the weakest. Moreover, [hmim][FEP] is more hydrophobic than [hmim] hexafluorophosphate ([PF6]), and the three solutes are mainly distributed around [FEP] anion.     

（e, 2e） Investigations of the Simultaneous Ionization and Excitation of Helium to He＋（n=2）

Three-Coulomb-wave method is employed to treat the process of （e, 2e） simultaneous ion- ization and excitation to the n=2 state of helium, with radial and angular correlated wave-function of He target. The triple differential cross sections are calculated and analyzed in very asymmetric coplanar geometry at incident energies of 5.50, 1.50 and 0.57 keV. Results are compared with the absolute measurements and the theoretical first and second Born approximation. The present triply differential cross section （TDCS） is found to be in good agreement with experimental data qualitatively. The distinguishing feature noted in TDCS structure is the presence of intense recoil peak that for certain parameters is even larger than the binary peak, an unusual feature for the single-ionization process at high and intermediate energies.     

Comparison study of several numerical integration schemes used in calculations of density functional theory

Several numerical integration schemes for the evaluation of matrix elements in density functional theory calculations have been studied and compared by computational practice. The best scheme was found to be the combination of the atomic partition function proposed by Becke with the scaled generalized Gauss-Laguerre quadrature formula for radial integration suggested by Yang, which achieve the highest convergence rate to the numerical integration. With the same number of integration points, the accuracy of the calculated results by this scheme is higher by 1 to 2 orders of magnitudes than that by other schemes. The reason for achieving higher accuracy by this scheme has been proposed preliminarily.     

Fukui Functions for the Temporary Anion Resonance States of Be~-, Mg~-, and Ca~-

In this work,the Fukui functions of the two ~2P resonance states of Be,a ~2P resonance state of Mg~–,and a ~2D resonance state of Ca~– have been determined.The trajectories of these resonance states,in conjunction with the complex rotation of the Hamiltonian,were used to determine their wave functions.The electron densities,Fukui functions,and values of the hyper-radiusr~2were computed from these wave functions.The Fukui functions have negative regions in the valence shell in addition to the inner shell regions,indicating screening effects of the outer temporary electron.Selected configuration interactions with up to quadruple excitations were used along the trajectories and for computing the final wave function.Based on this data,the densities,Fukui functions,andr~2were calculated.     

Theoretical Studies on Structures and Electron Affinities of 5-and 6-Halouracils

The molecular structures and electron affinities of 5-and 6-halouracils(XU,X=F,Cl,Br) were determined by means of five different density functional methods. The basis set used in this work is of double-ζ plus polarization(DZP) quality with additional diffuse s-and p-type functions,denoted DZP++. The geometries were fully optimized with each density functional theory(DFT) method,and discussed. Three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affin...     

DFT Investigation on the Insertion Reaction of an Isocyanide into the（Silyl）（silylene）molybdenum Si-C Bond

The chemistry of silylene-transition-metal complexes LnM(=SiR2)SiR3 is one of the attractive synthetic targets in organometallic chemistry for such complexes are key intermediates in many transition metal-catalyzed systems.In the present work,the novel insertion reactions of an isocyanide into the Cp*Mo(CO)2(=SiMe2)(SiMe3) Si-C bond were investigated extensively by using the DFT method.The effective core potentials(ECP) with a double-ζ valence basis set(LanL2DZ) were employed for Mo and Si and the standard 6-31G basis set for all other atoms.Polarization functions[22] were added for Si(ζd = 0.262),C(ζd = 0.8) and N(ζd = 0.8).The effect of solvent was evaluated with the standard PCM model.Our calculations show that the two-step channel is energetically favorable,and the solvation mode has minor influence on the relative energies.     

Three-dimensional quantum dynamics study of vibrational predissociation of HeI_2 van der Waals molecule for low vibrational excitation using the time-dependent wave packet method

Three-dimensional quantum mechanical calculations for vibrational predissociation of HeI2(B) van der Waals molecules are presented using the time-dependent wave packet technique within the golden rule approxima tion.The total and partial decay widths,lifetimes,rates and their dependence on initial vibrational states were obtained for HeI2 at low initial vibrational excited levels.Our calculations show that the calculated tota decay widths,lifetimes and rates agree well with those extrapolated from experimental data available The predicted total decay widths as a function of initial vibrational states exhibit highly nonlinear behavior.The very short propagation time (less.than 1 ps) required in the golden rule wave packet calculation is determined by the duration time of the final state inter-action between the fragments on the vibrationally deexcited adiabatic potential surface.The final state interaction between the fragments is shown to play an important role in determining the final rotational distri     

Coupling matrix element of electron self-exchange reactions in solution

On the basis of the common feature among the electron transfer process and the ion hydration process as well as the relevant experimental kinetic data of electron transfer reaction,a new accurate hydration potential function scheme for the determination of electron transfer coupling matrix element is presented.The coupling matrix element between two hydrated ions of the reacting system in solution is calculated.The results and the applicability of this scheme are discussed.