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

Based on the vibrational potential curves coupled with the minimum energy reaction path, the partial potential energy surface of the reaction I＋HI→IH＋I was constructed at the QCISD（T）//MP4SDQ level with pseudo potential method. And the formation mechanism of the scattering resonance states of this reaction was well interpreted with the partial potential energy surface. The scattering resonance states of this reaction should belong to Feshbach resonance because of the coupling of the vibrational mode and the translational mode. With the one-dimensional square potential well model, the resonance width and lifetime of the I＋HI（v=0）→IH（v＇=0）＋I state-to-state reaction were calculated, which preferably explained the high-resolved threshold photodetachment spectroscopy of the IHI- anion performed by Neumark et al..

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.

Exploration of Earth-Abundant Transition Metals(Fe,Co,Ni)Doped on W_(18)O_(49)System as Electrocatalysts for Urea Productiont

The conversion of inert N_(2)and CO_(2)into urea by electrocatalytic technology not only reduces the cost of urea synthesis in future,but also alleviatesthe environmental pollution problem caused by carbon emission in traditional industrial production.However,facing downside factors such as strong competitive reactions and unclear reaction mechanism,the design of high-performance urea catalysts is imminent.This study demonstrates that W_(18)O_(49)system doped heteronuclear metals(TM=Fe,Co,Ni)can effectively solve the problem of competitive adsorption between N_(2)and CO_(2)and realize the co-adsorption of N_(2)and CO_(2)at diverse sites.Their theoretical limiting voltages for urea production on TM-W_(18)O_(49)(TM=Fe,Co,Ni)systems are-0.46 V,-0.42 V and-0.52 V,respectively.The results are all lower than that of the contrastive voltage in pristine W_(18)O_(49)system(-0.91 V),further indicating the rationality and necessity of single-atom doped strategy for the co-reduction of two molecules.Specially,Co-W_(18)O_(49)can theoretically inhibit the side reactions of NRR,CO_(2)RR,and HER,which deserve future experimental exploration in future.The study suggests that doping heteronuclear metal into transition metal oxides is a feasible scheme to solve competitive adsorption and improve catalytic performance.

Understanding Bonding Nature of α-Keggin Polyoxometalates[XW_(12)O_(40)]^(n−)(X=Al,Si,P,S):A Generalized Superatomic Perspective

α-Keggin polyoxometalates(POMs)[XW_(12)O_(40)]^(n−)(X=Al,Si,P,S)are widely used in batteries owing to their remarkable redox activity.However,the mechanism underlying the applications appears inconsistent with the widely accepted covalent bonding nature.Here,first-principles calculations show that XW_(12)are core–shell structures composed of a shell and an XO_(4)^(n−)core,both are stabilized by covalent interactions.Interestingly,owing to the presence of a substantial number of electrons in W_(12)O_(36)shell,the frontier molecular orbitals of XW_(12)are not only strongly delocalized but also exhibit superatomic properties with high-angular momentum electrons that do not conform to the Jellium model.Detailed analysis indicates that energetically high lying filled molecular orbitals(MOs)have reached unusually high-angular momentum characterized by quantum number K or higher,allowing for the accommodation of numerous electrons.This attribute confers strong electron acceptor ability and redox activity to XW_(12).Moreover,electrons added to XW_(12)still occupy the K orbitals and will not cause rearrangement of the MOs,thereby maintaining the stability of these structures.Our findings highlight the structure–activity relationship and provide a direction for tailor-made POMs with specific properties at atomic level.

A Single-chain Antibody for One-pot Fabrication of Luminescent Gold Nanoclusters and Rabies Virus Imaging in Cells

The fragile antibody leads to a great challenge as a scaffold to fabricate the luminescent metal nanoclusters using one-pot method.This study presents a stable single-chain anti-body(scFv57R-ATS)for the fabrication of luminescent gold nanoclusters(AuNCs@scFv57R-ATS)and a quick,sensitive rabies virus detection in living cells.In this paper,AuNCs@scFv57R-ATS was designed to specifically recognize antigen RV in modified HeLa cells,which promoted the demonstration of metal nanocluster fluorescent probes for antigen targeting and therapy.