Table of Content

30 November 2009, Volume 30 Issue 11(1)

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Contents

Content of Chemical Journal of Chinese Universities Vol.30 No.11(Suppl.)(2009)

2009, 30(11(1)):  0. 

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Review

DFT Theoretical Studies on the Effects of Vanadium(V)-substitution on the Oxidative Property of α-Keggin\|type Heteropolyanion Clusters\|progress

WANG Jin-Yue*, FU Xiao-Hong, WANG Jian, HU Chang-Wei, XIONG Yan

2009, 30(11(1)):  1-8. 

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The redox properties of α-Keggin\|type heteropolyanion clusters [XM₁₂O₄₀]^n-(X=Si, P; M=Mo, W) mainly depend on their constituent outer metal\|oxygen cages {M₁₂O₃₆}. They are just as “reservoirs”, through which the transfer and transition of electrons and protons may occur. At the atomic and molecular level, the redox properties of these clusters can be controlled and also tuned by modifying the metal M on the cages and the central heteroatom X of the clusters. Combined with the experimental results, this review summarized our recent theoretical investigation of the vanadium-substitution on the redox properties of the Keggin anion clusters. Theoretical modeling and calculation results showed that the oxidative ability of the modified species was increased by partially substitution of the cage M atoms of the Keggin clusters by lower electronegativity of vanadium atoms. A linear correlation between the catalytic efficiency based on the vanadium atom and the micro\|structures of the vanadium(V)-substituted heteropolyanions [PV_nMo_12-nO₄₀]^(3+n)-(n=1-3) was established for the first time. This relationship may be suitable to interpret the catalytic behaviors of the title compounds in the benzene hydroxylation to phenol, and it's also preferable used in the reactions of the oxidative dehydrogenation of isobutyric acid, the nitration of the adamantine, etc. The establishment of this nearly linear structure\|property may lay the foundation of understanding and illustrating the behavior of the title compound in the homogeneous catalytic oxidation reactions, and may direct the catalysis design and the chosen of the catalytic reactions.  The results showed that the oxidative activity of the mono-vanadium\|substituted cluster was the highest among the titled species, while the oxidative activities of the di- and tri-vanadium-substituted clusters lied behind, with the former more active than the latter. Combined the calculated results with the available experimental electron reduction potentials(ERP) data, it was found that the Fermi energy levels(E_f) of these species change inversely with their ERPs, that is the E_f gets higher with increasing substituted vanadium number(n) of vanadium atom, the corresponding ERP gets smaller. Further calculations on the tungsten heteropolyanion clusters as the α-Keggin-type [XW₁₂O₄₀]^n-(X=Co^Ⅱ, Fe^Ⅲ, Si^Ⅳ, P^Ⅴ) also showed that the same relationship of E_f and ERP.

Articles

Docking to Explore the Interactions Between the Receptor TIR1 and Four Auxin Plant Hormones

JIA Xue-Bing, WANG Teng, SUN Hong-Wei*

2009, 30(11(1)):  9-15. 

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In this study, according to the classification and activity of auxin plant hormones the authors carry out docking experiments with four auxins, IAA, 1-NAA, 2,4-D, 2-NAA, and the receptor. The docking experiments are implemented step by step. First, the significant of co-factor InsP₆ and center water in the mechanism of auxins are explored by docking; second, the experiments that compared with the docking rusults of two situations involving fully rigid and selective flexible of active residue of the receptor TIR1 illuminate that selective flexibility docking by AutoDock4 reports more rational results, so that, AutoDock4 dockings are implemented with TIR1-Auxins; third, AutoDock4 docking by TIR1-Auxins-Aux/IAA illuminates that auxin as a molecular glue enhances the interaction between TIR1 receptor and Aux/IAA substrate by the weak interactions, such as hydrogen bond and hydrophobic interaction, furthermore, the weak interactions between receptor protein and ligands greatly influence on auxin activity of auxin ligands.

Theoretical Study on the Reaction Mechanism for Diels-Alder Cycloaddition of C₅₀(D_5h) with 1,3-Butadiene and 2,3-Disubstituted 1,3-Butadienes

XU Xiu-Fang*, SHANG Zhen-Feng, LI Rui-Fang, ZHAO Xue-Zhuang

2009, 30(11(1)):  16-22. 

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The reaction mechanism for Diels-Alder cycloaddition of C₅₀(D_5h) with 1,3-butadiene and 2,3-disubstituted 1,3-butadienes has been investigated using the semiempirical AM1 method. The calculated results show that: (1) All the Diels-Alder cycloaddition reactions take place via a concerted process. The length of the forming C—C bonds in transition states is in the range of 0.2293—0.2527 nm. (2) The activation energy(15.90 kJ/mol) for the cycloaddition of C₅₀(D_5h) with 1,3-butadiene is low. Moreover, this reaction is high exothermic of 402.50 kJ/mol. Therefore, it is predicted that not only kinetically but also thermodynamically the cycloaddition of C₅₀(D_5h) with 1,3-butadiene is easy to take place at room temperature. The C₅₀(D_5h) is more reactive than C₆₀ and C₇₀. (3) Different substituted groups on 1,3-butadiene have different effect on the reaction activation energy of the cycloaddition of C₅₀(D_5h) with substituted 1,3-butadiene. Weak electron-withdrawing or weak electron-donating groups have small effect on the reaction activation energy. While strong electron-withdrawing or strong electron-donating groups have outstanding effect on the reaction activation energy: Strong electron-donating groups obviously lower and strong electron-withdrawing group dramatically increase the reaction activation energy, respectively. (4) All the reverse reaction activation energies for the Diels-Alder cycloaddition of C₅₀(D_5h) with 1,3-butadiene and the substituted 1,3-butadienes are very high and in a range of 416.51—425.93 kJ/mol, indicating that the product of the Diels-Alder cycloadditions is very stable kinetically.

Molecular Dynamics Simulation of the Effect of Different Materials Surface on Natural Behavior of Nine Peptides of Coagulation Factor XII

LI Bo, ZHU Hao-Miao, WANG Ying, ZHAO Bo, LI Li*, SHEN Jian*

2009, 30(11(1)):  23-28. 

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Using NAMD with CHARMm force field, molecular dynamics simulations over 5 ns were applied to four different systems——single nine peptides of coagulation Factor XII(FXII), nine peptides of FXII with hydrophobic, hydrophilic or zwitterionic material. According to the analysis of the RMSD, conformational energy and dihedral energy etc, the zwitterionic material and hydrophilic material are suitable for keeping the natural behavior of nine peptides of FXII.

First-principles Study of Electronic Structure of Doped CuAlO₂

GAO Hai-Gen, ZHOU Jian, LU Ming-Hui*, CHEN Yan-Feng

2009, 30(11(1)):  29-32. 

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We used first-principles method to study the electronic properties and conductivity of CuAlO₂ doped with Mg, Be and S. The results show that the number of carriers increases and the effective masses reduce in the Mg doped CuAlO₂, which can explain the enhanced conductivity of CuAlO₂ by Mg doping observed in the experiment. We also calculated electronic structure of CuAlO₂ doped with Be and S, and found the results are similar to that of Mg doped one. It isbelieved that the Be and S doped CuAlO₂ also have higher conductivity than the pure one.

Theoretical Investigation on the Contact Resistance Between the Thiol Anchoring Group and the Gold Electrodes

YU Cui, ZHAO Jian-Wei*, LIU Hong-Mei

2009, 30(11(1)):  33-36. 

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The electronic transportation of a series of gold-sulfur atomic chains with different length was investigated theoretically by using density functional theory combined with nonequilibrium Green′s function method. The result shows that the conductance of gold wires with sulfur linking is larger than that of the pure gold atomic chains. In addition, the conductance keeps almost constant and does not decrease exponentially with the molecular chain length, which is different from the organic molecular wire. The results indicate that the sulfur group is well coupled to the gold electrode. As the molecule is anchored to the gold electrodes via the sulfur group in the junction, the contact resistance between the sulfur and gold electrode is small, and the junction resistance is mainly contributed by the molecule.

Theoretical Study of a Single Phthalocyanine Molecular Switch

JIANG Ning, SUN Shao-Rui, XIA Ding-Guo*

2009, 30(11(1)):  37-41. 

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In this paper, we theoretically investigate transport property of a metal-molecule-metal junction formed by phthalocyanine and gold chains through a combination of the density functional theory(DFT) and the nonequilibrium Green's function(NEGF) method. We find that the positions of the two protons in the center cavity affect the transport properties of the junction. In a bias voltage range between 1.8 V to 2.8 V, the current of α configuration(two protons align parallel to the gold chains) is obviously larger than that of β configuration(two protons aside the gold chains). The junction may potentially be used as electric switch in nanosized circuit, and moreover it may be applied to construct molecular logic gate device or high density nonvolatile memory.

Structural, Electronic and Magnetic Properties of Co_n-xMn_x(n=0—9, x=0—9) Clusters for Density Functional Calculations

DAI Xiao-Hong, YUAN Hong-Kuan, CHEN Hong*

2009, 30(11(1)):  42-51. 

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The density functional theory method was taken to study the structural evolution, electronic structures, and magnetic properties of Co_n-xMn_x(n=0—9, x=0—9) clusters. The results show that stabilities of CoMn clusters decrease with the increase of Mn concentration, and Co and Mn atoms tend to mix in structures to form more stable Co—Mn bonds. Cluster size, local structural environment, and Mn doping concentration have less effect on Co and Mn atomic magnetic moments, but magnetic ordering is sensitive to them. In low Mn doping CoMn clusters, clusters usually represent ferromagnetic coupling and about 2μ_B enhancement occurs as one Mn substitutes for one Co atom, whereas, intense antiferromagnetic coupling exists in high Mn doping CoMn

Studies on Hydroxamic Acid Histone Deacetylase Inhibitors(HDACI) by Molecular Docking and CoMFA

ZHANG Liang, XIANG Yu-Hong, Zhang Zhuo-Yong*

2009, 30(11(1)):  52-57. 

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Surflex-dock is used in docking histone deacetylase inhibitor and histone molecules. The interaction between ligand and receptor can revealed the binding mode of the inhibitors of HDAC. The result showed that the of docking has good correlation with the inhibitor activity. A further study on the three-dimensional quantitative structure-activity relationship(3D-QSAR) was carried out using the method of comparative mole-\{cular field analysis(CoMFA). The influences of different steps, probe atomic charge on model building were investigated. A 3D-QSAR model has been established, in which cross-validation coefficient q² is 0.668, and non-cross-validation correlation coefficient r² is 0.984. The established model has a good predictive ability, and it can be used to guide the drug design and synthesis.

Density Functional Theory Study for Epimerization of 2-Benzyl-2-ethoxycarbonyl-cyclopentanolate Ion

FENG Hua-Sheng, TIAN Yu, Sun Zhu-Fang, WANG Wen-Jun, HU Zhi-Biao, XIE Lun-Jia*

2009, 30(11(1)):  58-61. 

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DFT studies were carried out in order to investigate the epimerization of 2-benzyl-2-ethyoxyl-carbonyl-cyclopentanol in etherified reaction. Stationary structures and energy were obtained at the B3LYP/6-311+G(d,p) level. The loop will open when 2-benzyl-2-ethoxycarbonyl-cyclopentanol lose a H⁺, the —C—O^- group will turn into a aldehyde group, and the other carbon atom and the carbonyl composite a conjugate negative center. The energy of the trans conformation of the anion is 757 kJ/mol lower than the cis conformation, and the energy barrier of the conformation invert is only 305 kJ/mol. It shows the conformation invert reaction is controlled by thermodynamics and will happen easily. The result can explain the epimerization of 2-benzyl-2-ethoxycarbonyl-cyclopentanol in Williamson ether synthesis.

Theoretical Studies on Electronic Spectra and Nonlinear Optical Properties of Cyclometalated Platinum Complexes with β-Diketonate Ancillary Ligands

CHEN Jun-Rong, LI Quan*, ZHAO Ke-Qing

2009, 30(11(1)):  62-67. 

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DFT study on the electronic absorption spectra, second-order and third-order nonlinear optical properties of important phosphorescent materials: cyclometalated platinum complexes with β-Diketonate ancillary ligands are performed on Gaussian 03 package. Analysis on the frontier orbital of ground states shows that the electronic transition from the ground state to the first excited state are LLCT and MLCT transition. These complexes display good nonlinear optical properties. The predominant for second-order nonlinear optical properties is the charge transfer with π-π* character occurring between the left ligands. The third-order nonlinear optical properties is main determind by the charge transfer with d-π* character from metal Pt atom to β-Diketonate ancillary ligands, in addition, the transition between the left ligands is also play an important role.

DFT Study on the Catalytic Mechanism of Aspartoacylase and Hydrolysis Pathway of the Inhibitor

CHEN Xin, QIAO Qing-An*, JIN Yue-Qing, JING Jie, CAI Zheng-Ting, FENG Da-Cheng

2009, 30(11(1)):  68-72. 

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The hydrolysis mechanisms of N-acetyl-L-aspartate(NAA) and a potent inhibition of aspartoacylase, N-methylphosphono-L-aspartate(NMPA), were investigated by Density Functional Theory(DFT) of B3LYP method at 6-31G* basis level. The results indicated that the dynamical properties of the hydrolysis reactions for NAA and NMPA were similar. Both of them could be achieved through two possible reaction pathways: one was concerted and the other was stepwise, and the latter was the preferred on the potential energy surface. Compared with the reaction of NAA, the intermediate formed during the NMPA hydrolysis was more stable, and through which the NBO charges varied in a wider fluctuation. If NMPA occupied the active site, it could effectively inhibit the hydrolysis reaction of NAA.

Atomistic Simulations of Bauschinger Effect on Silicon Nanowire

MENG Qing-Yuan, JING Yu-Hang*

2009, 30(11(1)):  73-76. 

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Molecular dynamics simulations with Stillinger-Weber potential were used to study the Bauschinger effect on a single-crystalline silicon nanowire. In the case of uniaxial loading, the simulation results show that the uniaxial tensile and compressive loading exhibit asymmetry in mechanical property. Compared with those of compressive test, the higher Young's modulus and yield stress are obtained in the tension loading, which can be introduced by the free surface effect. Additionally, the plastic deformation due to tension loading is characterized by {111} slippages and rearrangements of atoms close to the necking region. In consideration of the Bauschinger effect, the compression-followed-by-tension process is applied to the silicon nanowire. It has been found that the reversal yield stress decreases and the Bauschinger effect increases with the increasing of the prestrain.

Study of Lowest Energy Structure About (GaN)_n(n=2—10) Clusters

LI En-Ling*, QI Wei, LI Xiao-Ping, ZHU Hong, YANG Chun-Yan, WANG Jin-Yu

2009, 30(11(1)):  77-82. 

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Geometric structure and relative stability of(GaN)_n(n=2—10) clusters were studied with the density functional-theory with 6-31G* basis sets of B3LYP. The geometric structures of ground state of (GaN)_n(n=2—10) clusters were obtained. The bond properties, photoelectron energy spectroscopy and polarizability of the isomers of (GaN)_n(n=2—10) clusters were calculated and analyzed. The results show that among the (GaN)_n(n=2—10) clusters, Ga₅N₅, Ga₉N₉ are more stable. The most structures of optimized (GaN)_n(n≤5) clusters are planar structure, and N—N bonds play a crucial role in stabilizing cluster. When n>6, the structures of optimized (GaN)_n(n=2—10) clusters are spacial structure. The Clusters exist in a large number of Ga—N bonds and form multi-ring structure, the ring structures of Ga and N play an important role with the increase of the number of total atoms.

DFT Study of the Electronic Structure in As(Ⅴ), Zn(Ⅱ)/TiO₂ System

XIA Shu-Wei, MA Xiao-Nan, YU Liang-Min, PAN Gang*

2009, 30(11(1)):  83-88. 

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Adsorbed species(DC double corner, SC single corner and SE single edge) in As(Ⅴ)-TiO₂ and Zn(Ⅱ)-TiO₂ system were calculated with DFT method to describe their electronic structural characters. The natural bond orbital analysis indicate that some obvious differences of the adsorption bonding mechanism were existed between As(Ⅴ) and Zn(Ⅱ) species on TiO₂ surface. For As(Ⅴ), it tend to form stable As—O σ bond with O atom of TiO₂ surface, but Zn(Ⅱ) always link with surface in a incompact style. The differences make the electronic delocalized degree of As(Ⅴ) adsorbed species being higher than Zn(Ⅱ), and it further results in a series differences with two system: vibrational spectra, charge distribution and the component of frontier orbital, etc.

Theoretical Investigation of CdX and ZnX(X=Te, Se, S)

XU Shu-Hong, WANG Chun-Lei, CUI Yi-Ping*

2009, 30(11(1)):  89-91. 

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Zinc blende and wurtzite structures CdX, ZnX(with X=Te; Se and S) clusters are investigated in this paper. The analyzed results show that the lowest vibrational frequencies, HOMO-LUMO gaps, dipole moment and Raman spectra present regular changes. The calculated absorption peaks shift to blue in order of CdTe, CdSe, CdS in CdX structures and ZnTe, ZnSe, ZnS in ZnX clusters. Finally, WBI values prove that Cd and Zn atoms have stronger interaction with Te atom than with Se and S atoms.

Structure and Character of the Dirner Between CH₃OS and HOCl

LI Zhi-Feng*, WANG Xiao-Yan, TANG Hui-An, ZHU Yuan-Cheng, LI Hong-Yu

2009, 30(11(1)):  92-95. 

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B3LYP/6-311++G** calculation is used to optimiz the structure of the complexes between CH₃OS and HOCl. The frequency analysis shows that there are nine stable complexes between the CH₃OS and HOCl (seven hydrogen bond complexes and two chlorine bond complexes). The interaction energies of complexes obtained by using MP2/6-311++G** method with BSSE corrected. Furthermore, the NBO and AIM analysis were applied to investigate the microcosmic mechanism and nature of the system.

PCM-TDDFT Study of the UV-Vis Spectra of Photochromic Spirooxazine and Spiropyran Compound

LIN Bing, CAI Ming , LI Wei*

2009, 30(11(1)):  96-102. 

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Photochromic compounds and polymer are new functional materials, which can be widely used in optical information storage, optical conversion devices, optical switches and other fields. In this paper, the electronic absorption spectra of 21 spriooxazine and spiropyran derivatives in close and open-ring states were investigated in the framework of time-dependent density functional theory(TDDFT) with polariable continuum model(PCM) including solvent effect. The B3LYP and PBE0 hybrid functionals together with 6-31+G(d) basis set were selected to calculate the excitation energies of 8—30 lowest-lying singlet excited states. In close-ring states, both PBE0 and B3LYP functional well reproduce the experimental values, and the mean absolute error(MAE) are 0.16 and 0.20 eV, respectively. The mainly absorption bands mainly raise from the π→π* transition from HOMO-1, HOMO to LUMO, LUMO+1. In open-ring states, both PBE0 and B3LYP overestimate the experimental excitation energies by 0.08—0.40 eV, and the MAE is 0.28 and 0.22 eV, respectively. Calculations reveal that the maximum absorption bands mainly result from the transition from HOMO or HOMO-1 to LUMO, and have π→π* characters.

Quantum Chemical Calculations on pK_a Values of Oranic Compounds in Aqueous Solution

DING Xiao-Qin*, SUN Yang, DING Jun-Jie, CHEN Ji-Sheng

2009, 30(11(1)):  103-108. 

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Quantum chemical calculations of the pK_a values were performed using DFT method with 6-31+g(d,p) basis set for more than 200 compounds of alcohol, phenol, carboxylic acid, aliphatic amines, aromatic amine and nitrogen heterocyclics etc. The solution-phase calculations use polarized continuum solution(PCM) model with default set in water. The residue of most compounds is less than 1 pK_a unit. Correlation coefficient between experiment results and forecast results is better than 094. The results can help us to research reaction activity difference between different molecules or different groups in one molecule. Quantum Chemical calculations of the pK_a values will be instructive to computer aided molecular design and organic synthetic route design and optimization.