Theoretical Study on GSH Activation Mechanism of a New Type of Glutathione Transferase Gtt2

Glutathione transferases（GSTs） play an important role in the detoxification of xenobiotic/endobiotic toxic compounds. The α-, π-, and/l-classes of cytosolic GSTs have been studied extensively, while Gtt2 from Saccharo- myces cerevisiae, a novel atypical GST, is still poorly understood. In the present study, we investigated the gluta- thione（GSH） activation mechanism of Gtt2 using the density functional theory（DFT） with the hybrid functional B3LYP. The computational results show that a water molecule could assist a proton transfer between the GSH thiol and the N atom of His133. The energy barrier of proton transfer is 46.0 kJ/mol. The GSH activation mechanism and the characteristics of active site are different from those of classic cytosolic GSTs.

Theoretical Study on the Addition Reactions of Benzaldoximes with Propene

The Michael addition reactions of Z and E benzaldoximes with propene were investigated theoretically by DFT method at B3LYP/6-31G^＊ level. The calculation results show that both addition reactions are concerted processes accompanied by the migration of hydrogen from the atom oxygen to carbon. Both products Z and E nitrones have dipolar charge distributions and activities. Z isomer is more favorable in the reaction due to the barrier is lower.

Theoretical Investigation on the Luminescent Properties of Polyfluorene and Poly(fluorene-co-thiophene)

The density functional theory was employed to study the structures, ionization potentials（IPs）, electron affinities（EAs）, and HOMO-LUMO gaps（ΔH-L） of the oligomers. The time-dependent density functional theory（TD-DFT） and ZINDO were employed to study the lowest excitation energies（Egs） and the absorption and emission spectra of the oligomers of polyfluorene（PF） and poly（fluorene-co-thiophene）（PFT）. By extrapolating ΔH-L and Egs to those of infinite chain length, band gaps and effective conjugation lengths of the corresponding polymers were obtained. The IPs, EAs and 2abs of the polymers were obtained by extrapolating those of the oligomers to the inverse chain length equal to zero（I/n=0）. The outcome shows the decreased dihedral angle between fluorene and thiophene units in the PFT compared to that between fluorene units in the PF results in the increased efficient conjugation of PFT. These cause both the maximal absorption and emission wavelengths of PFT red-shifted compared with those of PF.

Study of the Electrical Double Layer of a Spherical Micelle: Functional Theoretical Approach

By using the iterative method in functional theory, an analytic expression of the Poisson-Boltzmann equation (PB eq.), which describes the distribution of the potential of electrical double layer of a spherical micelle, has been carried out under the general potential condition for the first time. The method also can give the radius, the surface potential, and the thickness of the layer.

Theoretical Research on Scattering Resonance States of Reaction I＋HI（v=O）→IH（v＇=0）＋I： Partial Potential Energy Surface and One-dimensional Quantum Reactive Scattering Calculation

把最小的精力反应路径基于结合的震动的潜在的曲线，反应 I+HIIH+I 的部分势能表面在 QCISD (T) 被构造 // 有假潜力的 MP4SDQ 水平方法。并且散布回声的形成机制这声明反应很好与部分势能表面被解释。因为联合震动的模式和翻译模式，这反应的散布回声状态应该属于 Feshbach 回声。与一个维的方形的潜在的井模型，回声宽度和 I+HI (=0 ) IH 的一生一起(“ =0 )+I state-to-state 反应被计算，它最好解释 IHI 阴离子的解决高度的阀值 photodetachment 光谱学由 Neumark 等表现了……

The theoretical study of one-carbon unit transfer with H_2O participation from imidazolidine to dUMP analogue

The ONIOM quantum mechanics method is used to study the reaction of one-carbon unit transfer from an imidazolidine to 6- aminouracil model with the participation of water molecules.The computation results show that in this reaction the participation of H_2O molecule makes the energy barrier lower because of the H-bond interaction.

Theoretical Study of the Scattering Resonance State, Reaction Mechanism and Partial Potential Energy Surface of the F+CH4→HF+CH3 Reaction

The partial potential energy surface was constructed by ab initio method [QCISD（T）/6- 311＋＋G（2df,2pd）]for F＋CH4→HF＋CH3 reaction system. It not only explained the reaction mechanism brought forward by Diego Troya by means of quasiclassical trajectory （QCT） but also successfully validated Kopin Liu＇s experimental phenomena about the existence of the reactive resonance. The lifetime of the scattering resonance state was about 0.07 ps. All these were in agreement with the experiments.

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-（plus polariza- tion（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 affinity（AEA）, the vertical electron affinity（VEA）, and the vertical detachment energy（VDE）. An excellent agreement between our B3LYP results and those obtained by other calculations regarding the structural modifications and electron affinities of neutral and anion 5XU was found. The differences in charge distribution between uracil and halogenated uracils were indicated, thus the ability to form the hydrogen bonds of halogenated uracils was discussed. It shows the applicability of the DFT/DZP＋＋ method to predict the similar molecular models at a highly economical computational cost.

Theoretical Studies on Structural and Spectroscopic Properties of Photoelectrochemical Cell Ruthenium Sensitizers―the Derivatives of N3

A series of dye molecules was designed theoretically.Particularly,azoles and their derivatives were chosen as the modifying groups linking to ancillary ligands of [Ru（dcbpyH2）2（NCS）2]（N3,dcbpy=4,4＇-dicarboxy2,2＇-bipyridine;NCS=thiocyanato）.Density functional theory（DFT） based approaches were applied to exploring the electronic structures and properties of all these systems.The dye molecule with 1,2,4-triazole groups which exhibits a very high intensity of absorption in visible region,was obtained.Time-dependent DFT（TD-DFT） results indicate that the ancillary ligand dominates the molecular orbital（MO） energy levels and masters the absorption transition nature to a certain extent.The deprotonation of anchoring ligand not only affects the frontier MO energy levels but also controls the energy gaps of the highest occupied MO（HOMO） to the lowest unoccupied MO（LUMO） and LUMO to LUMO＋1 orbital.If the gap between LUMO-LUMO＋1 is small enough,the higher efficiency of dye-sensitized solar cell（DSSC） should be expected.

Inhibition Mechanism of Cholinesterases by Carbamate: A Theoretical Study

The density functional theory at the B3LYP/6-311G（d, p） level was applied to exploring the inhibition mechanism of cholinesterases by carbamate. The results indicate that the inhibition reactions with or without the catalytic effect of the catalytic triad in eholinesterases underwent a two-step addition-elimination mechanism, which is in good agreement with the proposed mechanism. The solvent has a strong effect on the inhibition reactions and the reaction with the catalytic triad in the solvent phase is close to the real reaction under biological condition.

Theoretical Design of Catalytic Domain of Abzyme Se-scFv2F3 by Introducing a Catalytic Triad

The single chain antibody scFv2F3 can be converted into selenium-containing Se-scFv2F3 by chemical mutation of the Ser residues. With antibody fragment 1NQB as a template, the catalytic domain of scFv2F3 was built by using homology modeling and molecular dynamics（MD） simulations. On the basis of the 3D model, we discussed the importance of Ser52 as the chemical modification site and redesigned the protein groups nearby Ser52 via intro- ducing a catalytic triad. The following 10 ns MD results show that the designed Ser52-Trp29-Gln72 catalytic triad is stable enough and high close to the local structural features of native glutathione peroxidases（GPX）. Our results may be useful for creating a new abzyme with higher catalytic efficiency and stability.

Discrimination of Glycine Enantiomers by the Biologically Important Phosphocompounds:A Theoretical Prediction

With the aid of high-level B3LYP and MP2 calculations, three new neutral structures of glycine （iin, ivn and vn, see Fig. 2） were obtained and validated by frequency calculations. The structural and energetic analyses showed that iin, ivn and vn are enantiomers to the previous IIn, IVn and Vn （J. Am. Chem. Soc. 1992, 114, 9568.）, respectively. Owing to the presence of these novel conformers, a redistribution of the populations of glycine conformers is resulted in and causes the remarkable decrease of the most stabilized Ip （from 48% to 38%）. It indicated that the simple glycine molecule can show chirality under certain conditions. The interacting modes of glycine enantiomeric pairs （e.g., ivn and IVn） with PG showed large differences （Fig. 4）; in addition, their interaction energies corrected with basis set superposition errors （BSSE） were calculated to be --66.81 and -46.99 kJ tool^-1, respectively. Accordingly, the glycine enantiomers can be potentially applied to the chiral recognition in biological and pharmaceutical areas.

Solution of the Poisson-Boltzmann Equation for a Cylindrical Particle with a Limited Length: Functional Theoretical Approach

With the help of the method of separation of variables and the Debye-Hüchel approximation, the Poisson-Boltzmann equation that describes the distribution of the potential in the electrical double layer of a cylindrical particle with a limited length has been firstly solved under a very low potential condition. Then with the help of the functional analysis theory this equation has been further analytically solved under general potential conditions and consequently, the corresponding surface charge densities have been obtained. Both the potential and the surface charge densities cointide with those results obtained from the Debye-Hüchel approximation when the very low potential of zeψ〈〈kT is introduced.

Theoretical Studies of Water’s and Methanol’s Effects on Alcoholysis of N-Benzyl-3-oxo-β-sultam

The mechanisms about the water’s and methanol’s effects on the alcoholysis of N-benzyl-3-oxo-β-sultam together with their differences have been studied by using density func- tional theory at the B3LYP/6-31G＊ level. The results, in comparison with a previous study on the relative reaction without the assistance of water and methanol, show that the added water or methanol can remarkably reduce the energy barrier of alcoholysis reaction of N-benzyl-3-oxo- β-sultam and the most favorite pathway is the breaking of C–N bond instead of S–N. It is also found that the reaction energy barrier of methanol-assisted alcoholysis is a little higher than that of the water-assisted one.

Theoretical studies on the one-and two-photon absorption properties of azulenylporphyrins and azulene-fused porphyrins

The electronic structures, one-photon absorption （OPA） and two-photon absorption （TPA） properties of the azulenylporphyrins and azulene-fused porphyrins have been comparatively studied by using DFT/B3LYP/6-31G（d） and the ZINDO/SDCI method. With the number of azulenyl groups increasing, the OPA wavelengths of all molecules are red-shifted in 400-600 nm and the two-photon absorption cross section is gradually enlarged. The azulene-fused structures facilitate an expanding conjugated area and increasing TPA cross section. The origin of TPA properties of studied compounds is studied with a two-level model. In summary, the azulene-fused porphyrins exhibit strong two-photon absorption.

Relative Responses of Noble Gases Using a Pulsed Discharge Helium Photoionization Detector:Theoretical Calculation and Experimental Determination

The relative response factors（RRFs） for noble gas（Ng） were determined on a pulsed discharge helium photoionization detector. Using ab initio method, the atomic orbitals of noble gas were calculated and used to determine the number of ionizable electrons on the basis of the continuous emission of He2. The molar responses of noble gases is well correlated with the number of ionizable electrons.

Theoretical prediction of the optimal conditions for observing the stereodynamical vector properties of the C(~3P) + OH(X^2Π) → CO(X^1 Σ^+) + H(~2S) reaction

The best optimal initial reactant state and collision energy for observing the stereodynamical vector properties of the title reaction in the ground electronic state X2A’ potential energy surface （PES）[Zanchet et al. 2006 J. Phys. Chem. A 110 12017] are theoretically predicted using the quasi-classical trajectory （QCT） method for the first time. The calculated results reveal that the smallest value of the rotational quantum number j, larger vibrational quantum number v, and the lower strength of collision energy should be selected for offering the most obvious picture about the stereodynamical vector properties. Polarization-dependent differential cross sections and the angular momentum alignment distribution, P（θr） and P（Φr） in the center-of-mass frame, are obtained to gain an insight into the alignment and orientation of the product molecules. The rotational angular momentum vector j’ of CO is aligned to be perpendicular to reagent relative velocity k. The product polarizations align along the y axis, pointing to the positive direction of the y axis. A new method is developed to investigate massive reactions with various initial states and to further study the vector properties of the fundamental reactions in detail.

Splitting of Degenerate Superatomic Molecular Orbitals Determined by Point Group Symmetry

We first confirm an idea obtained from first-principles calculations,which is in line with symmetry theory:Although superatomic molecular orbitals(SAMOs) can be classified according to their angular momentum similar to atomic orbitals,SAMOs with the same angular momentum split due to the point group symmetry of superatoms.Based on this idea,we develop a method to quantitatively modulate the splitting spacing of molecular orbitals in a superatom by changing its structural symmetry or by altering geometric parameters with the same symmetry through expansion and compression processes.Moreover,the modulation of the position crossover is achieved between the lowest unoccupied molecular orbital and the highest occupied molecular orbital originating from the splitting of different angular momenta,leading to an effective reduction in system energy.This phenomenon is in line with the implication of the Jahn–Teller effect.This work provides insights into understanding and regulating the electronic structures of superatoms.

Ultrahigh Harmonic Generation from an Atom with Superposition of Ground State and Highly Excited States

我们从在地面状态和高度激动的状态的重叠准备的一个原子调查高顺序的泛音产生。当原子被超短波的脉搏照耀时，在泛音光谱的高原的截止位置大部分与原子开始处于扎根的状态的案例相比被扩大。thehigh 顺序泛音高原的延期的物理能被原子起始的波浪包的空间结构解释。我们能由代替高度激动的一些的特别协调重叠说形成一个空间地局部性的激动的波浪包的激动的州的论坛优化高顺序的泛音的产生。

Harmonic Enhancement Mechanism of a Superposition State Atom Irradiated by Short Pulses

我们调查其起始的状态在它的扎根的状态和一个激动的状态的重叠被准备的一个模型原子的高顺序的泛音产生(HHG ) 由不同持续时间激光脉搏照耀。比作从其起始的状态处于它的扎根的状态的一个原子产生的 HHG，它的变换效率获得某改进。改进从更高的电离率发源(而非电离收益) 有重叠的原子起始的状态。