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 Design of Blue-light-emitting Material Based on 1,2,3-Benzotriazole-based Derivative

Theoretically,1,2,3-benzotriazole（BT）-based derivative is designed by the struc-tural tuning in 2,1,3-benzothiadiazole（BTD）-based derivative and presents potential for applications in organic light-emitting diodes（OLEDs）.Calculations show that the emission spectrum of BT-based derivative is located at the blue scope,so it can act as a blue-light-emitting material.Importantly,the oscillator strength of emission spectrum is significantly enhanced by replacing BTD with BT,implying it possess large fluorescent intensity.Additionally,BT-based derivative exhibits improved hole transportation with respect to the BTD-based derivative.

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.

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 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.

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.

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.

Rotational Isomeric State Model of Poly(vinylidene chloride) Based Upon ab Initio Electronic Structure Calculations

The rotational isomeric state（RIS） model was constructed for poly（vinylidene chloride）（PVDC） based on quantum chemistry calculations. The statistical weighted parameters were obtained from RIS representations and ab initio energies of conformers for model molecules 2,2,4,4-tetrachloropentane（TCP） and 2,2,4,4,6, 6-hexachloroheptane（HCH）. By employing the RIS method, the characteristic ratio C∞ was calculated for PVDC. The calculated characteristic ratio for PVDC is in good agreement with experiment result. Additionally, we studied the influence of the statistical weighted parameters on C∞ by calculating δC∞/δlnw. According to the values of δC∞/δlnw, the effects of second-order Cl-CH2 pentane type interaction and C1--C1 long range interaction on C∞ were found to be important. In contrast, first-order interaction is unimportant.

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.

Oxygen Atom Exchange Mechanism in Reaction of OH Radical with AsO

Oxygen atom exchange reaction mechanism in the reaction of OH radicals with AsO was investigated by means of the density functional theory (DFT) with 6 311++G( 3df,3pd ) and 6 311++G( d,p ) basis sets. The calculated results suggest that the reaction between OH and AsO should make the oxygen atoms exchange rapidly because the barrier to isomerization is significantly less than the HO-AsO bond dissociation energy.

Investigation of hydrogen bonding in neat dimethyl sulfoxide and binary mixture(dimethyl sulfoxide + water) by concentration-dependent Raman study and ab initio calculation

In this study, our vibrational spectroscopic analysis is made on hydrogen-bonding between dimethyl sulfoxide and water comprises both experimental Raman spectra and ab initio calculations on structures of various dimethyl sulfoxide/water clusters with increasing water content. The Raman peak position of the v（S=O） stretching mode of dimethyl sulfoxide serves as a probe for monitoring the degree of hydrogen-bonding between dimethyl sulfoxide and water. In addition, the two vibrational modes, namely, the CH3 symmetric stretching mode and the CH3 asymmetric stretching mode have been analysed under different concentrations. We relate the computational results to the experimental vibrational wavenumber trends that are observed in our concentration-dependent Raman study. The combination of experimental Raman data with ab initio calculation leads to a better knowledge of the nature of the hydrogen bonding and the structures of the hydrogen-bonded complexes studied.

Investigation of inter-molecular hydrogen bonding in the binary mixture (acetone+water) by concentration dependent Raman study and ab initio calculations

This paper reports that vibrational spectroscopic analysis on hYdrogen-bonding between acetone and water comprises both experimental Raman spectra and ab initio calculations on structures of various acetone/water complexes with changing water concentrations. The optimised geometries and wavenumbers of the neat acetone molecule and its complexes are calculated by using ab initio method at the MP2 level with 6-311＋G（d,p） basis set. Changes in wavenumber position and linewidth （fullwidth at half maximum） have been explained for neat as well as binary mixtures with different mole fractions of the reference system, acetone, in terms of intermolecular hydrogen bonding. The combination of experimental Raman data with ab initio calculation leads to a better knowledge of the concentration dependent changes in the spectral features in terms of hydrogen bonding.

Adsorptions and diffusions of carbon atoms on the surface and in the subsurface of Co(200): A first-principles density-functional study

First-principles calculations based on density functional theory are used to investigate the adsorptions and diffusions of carbon atoms on the surface and in the subsurface of Co （200）. The preferred site for the carbon atom on the surface is the hollow site, and the preferred site in the subsurface is the octahedral site. There is charge transfer from the surface to the adsorbed carbon atom, and for the most favorable adsorbed structure the charge transfer is largest. Moreover, the energy barriers for the diffusions of carbon atoms on the surface and from the surface into the subsurface and then back to the surface are calculated in detail. The results indicate that the energy barrier for the diffusion of carbon atoms on the surface is comparable to that from the subsurface to the surface. The results imply that both the direct surface nucleation and the surface segregation from Co bulk can be observed in the chemical vapor deposition growth of graphene on Co （200） substrate, which can gain a new insight into the growth mechanism of graphene.

Insight into Reaction Mechanism of Sirtuins via Molecular Simulation and Density Functional Theory Study

With density functional theory（DFT） and molecular mechanics method, the catalytic mechanism of silent information regulator（sirtuins） has been investigated. The calculations support the SN2-1ike reaction of the initial step of the catalysis, and are consistent with experiment results. We further explored the second step of the catalysis and proposed that this step took place in a concerted reaction. In addition, the side chain of Phenylalanine33 may help to shield the glycosidic bond from water and be in a position to protect the developing oxacabenium transition state from hydrolysis. Our results of the calculations support this hypothesis that the phenylalanine33 plays a critical role in the sirtuins biology function.

Effects of the structural order of canthaxanthin on the Raman scattering cross section in various solvents:A study by Raman spectroscopy and ab initio calculation

In this work,we measure the Raman scattering cross sections（RSCSs） of the carbon-carbon（CC） stretching vibrational modes of canthaxanthin in benzene,acetone,n-heptane,cyclohexane,and m-xylene.It is found that the absolute RSCS of CC stretching mode of canthaxanthin reaches a value of 10 24 cm ^-2 ·molecule ^-1 ·sr ^-1 at 8×10 ^-5 M,which is 6 orders of magnitude larger than general RSCS（10 30 cm 2 ·molecule 1 ·sr 1）,and the RSCSs of canthaxanthin in various solvents are very different due to the hydrogen bond.A theoretical interpretation of the magnetic experimental results is given,which is introduced in a qualitative nonlinear model of coherent weakly damped electron-lattice vibration in the structural order of polyene chains.In addition,the optimal structure and the bond length alternation（BLA） parameter of canthaxanthin are calculated using quantum chemistry calculation（at the b3lyp/6-31g（d,p） level of theory）.The theoretical calculations are in good agreement with the experimental results.Furthermore,the combination of Raman spectroscopy and the quantum chemistry calculation study would be a quite suitable method of studying the structures and the properties of the π-conjugated systems.

Influence of Solid-liquid Interaction and Temperature on the Dynamic Dewetting of a Thin Polymer Film:A Molecular Dynamics Study

Coarse-grained molecular dynamics simulations were carried out to investigate the dewetting behavior of a polymer thin film on partial wetting solid surface at the early stage of the dewetting process. Spontaneous dewetting is initiated by removing a band of strip from both the ends of the liquid polymer film which has achieved equilibrium. The solid-liquid interaction and temperature were varied to show their influence on the dewetting dynamics during dewetting as well as the shape evolution of the liquid polymer film. As is consistent with the results obtained in previous researches, the liquid film recedes at a constant speed initially with different solid-liquid couplings and tempe- ratures. Furthermore, smaller coupling parameters or higher temperatures tend to accelerate the recession speed of the liquid film and shorten the constant-speed recession duration. Obvious rims were not always observed. Both coupling parameter and temperature can influence the emergence of the rims.

Association of (S)-Isoserine Derivatives and 2,2,4-Trimethyl-3-hydroxy-4-cyclohexenecarboxylate

Two novel compounds（4a and 4b） were obtained by the association of 2,2,4-trimethyl-3-hydroxy-5-cyclohexenecarboxylate with （S） -isoserine derivatives. The space location of the hydroxyl group of compound 1 was identified via the formation of lactone 6. Fe2 （SO4）3·xH2O was used as the catalyst for the synthesis of lactone 6. The carboxyl group was selectively protected with diazomethane. All the products were characterized via ^1H NMR and mass spectra. The Docking study showed that the associations have the potential therapeutic use of DPP-Ⅳ inhibitor.

Effect of Some Metal Ion Dopants on Electrochemical Properties of Ni(OH)_2 Film Electrode

The Ni(OH) 2 film electrodes doped respectively with alkali-earth metal aluminum, lead, partial transition metal and some rare-earth metal(altogether 17 kinds of metals) ions were prepared by cathode electrodeposition. The electrode reaction reversibility, the difficult extent of oxygen evolution, the proton diffusion coefficient, the discharge potential of middle value and the active material utilization of the Ni(OH) 2 film electrode were compared with those of the ones doped with the metal ions by means of cyclic voltammetry, potential step and constant current charge-discharge experiments. It was found that Ca 2+ , Co 2+ , Cd 2+ , Al 3+ etc. have obviously positive effect.

Spectra of Linear Polyene Molecule-canthaxanthin

Raman spectra and ultraviolet-visible（UV-Vis） absorption spectra of linear polyene molecule-canthaxan-thin in n-hexane are measured and analyzed.In addition,the optimized structure of canthaxanthin was calculated via density functional theory（DFT） functional B3LYP.With decreasing the concentration,Raman scattering cross section （RSCS） of fundamental frequency is extremely high,and the UV-Vis absorption bands become narrower.The results of coherent weakly damped electron-Lattice vibration model were analyzed.

Fragmentation Behavior and Ionization Potentials of Lead Clusters Pb_n(n≤30)

The properties of Pbn（n=2―30） clusters including binding energies,second differences in energy,and HOMO-LUMO gaps,especially fragmentation energies and ionization potentials,have been studied by ab initio calculation.The main fragmentation products of Pbn＋ are shown to be Pb＋Pbn-1＋ for n≤14 and two small cluster fragments for larger ones with n14.The Pb13＋ appears frequently as the products in the fragmentations of large clusters.Also,the calculated ionization potentials of the clusters are consistent with the experiment data.