Biomedical subjects

Ze-Sheng Li

Publications and source records attributed to Ze-Sheng Li.

At least 37 records · Page 2Linked to original sources

PubMed2005

The effects of Lowe-Andersen temperature controlling method on the polymer properties in mesoscopic simulations.

Lowe-Andersen (LA) temperature controlling method [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] is applied in a series of mesoscopic polymer simulations to test its validity and efficiency. The method is an alternative for dissipative particle dynamics simulation (DPD) technique which is also Galilean invariant. It shows excellent temperature control and gives correct radial distribution function as that from DPD simulation. The efficiency of LA method is compared with other typical DPD integration schemes and is proved to be moderately efficient. Moreover, we apply this approach to diblock copolymer microphase separation simulations. With LA method, we are able to reproduce all the results from the conventional DPD simulations. The calculated structure factors of the microphases are consistent with the experiments. We also study the microphase evolution dynamics with increasing chiN and find that the bath collision frequency Gamma does not affect the order of appearing phases. Although the thermostat does not affect the surface tension, the order-disorder transition (ODT) is somewhat sensitive to the values of Gamma, i.e., the ODT is nonmonotonic with increasing Gamma. The dynamic scaling law is also tested, showing that the relation obeys the Rouse theory with various Gamma.

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PubMed2005

Theoretical study and rate constant calculation for the reactions of SH (SD) with Cl2, Br2, and BrCl.

The mechanisms of the SH (SD) radicals with Cl2 (R1), Br2 (R2), and BrCl (R3) are investigated theoretically, and the rate constants are calculated using a dual-level direct dynamics method. The optimized geometries and frequencies of the stationary points are calculated at the MP2/6-311G(d,p) and MPW1K/6-311G(d,p) levels. Higher-level energies are obtained at the approximate QCISD(T)/6-311++G(3df, 2pd) level using the MP2 geometries as well as by the multicoefficient correlation method based on QCISD (MC-QCISD) using the MPW1K geometries. Complexes with energies less than those of the reactants or products are located at the entrance or the exit channels of these reactions, which indicate that the reactions may proceed via an indirect mechanism. The enthalpies of formation for the species XSH/XSD (X = Cl and Br) are evaluated using hydrogenation working reactions method. By canonical variational transition-state theory (CVT), the rate constants of SH and SD radicals with Cl2, Br2, and BrCl are calculated over a wide temperature range of 200-2000 K at the a-QCISD(T)/6-311++G(3df, 2pd)//MP2/6-311G(d, p) level. Good agreement between the calculated and experimental rate constants is obtained in the measured temperature range. Our calculations show that for SH (SD) + BrCl reaction bromine abstraction (R3a or R3a') leading to the formation of BrSH (BrSD) + Cl in a barrierless process dominants the reaction with the branching ratios for channels 3a and 3a' of 99% at 298 K, which is quite different from the experimental result of k3a'/k3' = 54 +/- 10%. Negative activation energies are found at the higher level for the SH + Br2 and SH + BrCl (Br-abstraction) reactions; as a result, the rate constants show a slightly negative temperature dependence, which is consistent with the determination in the literature. The kinetic isotope effects for the three reactions are "inverse". The values of kH/kD are 0.88, 0.91, and 0.69 at room temperature, respectively, and they increase as the temperature increases.

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PubMed2005

Theoretical study on the reaction mechanism of the methyl radical with nitrogen oxides.

The radical-molecule reaction mechanism of CH3 with NOx (x = 1, 2) has been explored theoretically at the B3LYP/6-311Gd,p and MC-QCISD (single-point) levels of theory. For the singlet potential energy surface (PES) of the CH3 + NO2 reaction, it is found that the carbon to middle nitrogen attack between CH3 and NO2 can form energy-rich adduct a (H3CNO2) with no barrier followed by isomerization to b1 (CH3ONO-trans), which can easily convert to b2 (CH3ONO-cis). Subsequently, starting from b (b1, b2), the most feasible pathway is the direct N-O bond cleavage of b (b1, b2) leading to P1 (CH3O + NO) or the 1,3-H-shift and N-O bond rupture of b1 to form P2 (CH2O + HNO), both of which may have comparable contribution to the reaction CH3 + NO2. Much less competitively, b2 can take a concerted H-shift and N-O bond cleavage to form product P3 (CH2O + HON). Because the intermediates and transition states involved in the above three channels are all lower than the reactants in energy, the CH3 + NO2 reaction is expected to be rapid, as is consistent with the experimental measurement in quality. For the singlet PES of the CH3 + NO reaction, the major product is found to be P1 (HCN + H2O), whereas the minor products are P2 (HNCO + H2) and P3 (HNC +H2O). The CH3 + NO reaction is predicted to be only of significance at high temperatures because the transition states involved in the most feasible pathways lie almost above the reactants. Compared with the singlet pathways, the triplet pathways may have less contributions to both reactions. The present study may be helpful for further experimental investigation of the title reactions.

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PubMed2005

Dual-level direct dynamics studies on the reaction Cl + CHBr(2)Cl.

Theoretical investigations are carried out on the multichannel reaction CHBr(2)Cl + Cl by means of direct dynamics methods. The minimum energy path (MEP) is obtained at the BH&H-LYP/6-311G(d,p) level, and energetic information is further refined at the CCSD(T)/6-311+G(2df,2p) (single-point) level. The rate constants for three reaction channels, H-abstraction, Br-abstraction, and Cl-abstraction, are calculated by using the improved canonical variational transition state theory (ICVT) incorporating with the small-curvature tunneling (SCT) correction. The theoretical overall rate constants are in good agreement with the available experimental data and are found to be k=2.58 x 10(-15) T(1.18) exp(-861.17/T) cm(3)molecule(-1)s(-1) over the temperature range 200--2400 K. For the title reaction, H-abstraction reaction channel is the major channel at the lower temperatures, while as the temperature increases, the contribution of Br-abstraction reaction channel should be taken into account. At 2180 K, the rate constants of these two pathways are equal. Cl-abstraction reaction channel is minor channel over the whole temperature region.

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PubMed2004

Homology modeling and S(N)2 displacement reaction of fluoroacetate dehalogenase from Burkholderia sp. FA1.

Fluoroacetate dehalogenase (EC 3.8.1.3) catalyzes the dehalogenation of fluoroacetate and other haloacetates. In order to investigate the relation between the structure and the function, and understand the reaction mechanism of the enzyme, a 3D model of fluoroacetate dehalogenase FAc-DEX FA1 was built by homology-based modeling. The 3D model was optimized by unconstrained molecular dynamics simulation. Furthermore, the optimized 3D model was assessed by comparison of specific properties with two known protein structures. From the final 3D model, we find that the main residues involved in the active site in FAc-DEX FA1 were Phe34, Trp148, Tyr147, Tyr212, Asp104, and His271; especially Asp104 was the key nucleophilic residue in substrate binding. A reaction model including Asp104 and the substrate fluoroacetate was then constructed and used to characterize explicit enzymatic reactions. In order to further illustrate catalytic properties, the equilibrium geometries, energies, and frequencies of stationary points (reactants, products, and transition states) of the reaction model were calculated at the B3LYP/6-31G level of theory in both gas phase and solution. The results showed that the reaction in gas was dynamically more favorable than in solution.

Amino Acid Sequence↗

PubMed2004

Theoretical study on reaction mechanism of the fluoromethylene radical with nitrogen dioxide.

The complex doublet potential energy surface for the reaction of 1CHF with NO2, including 14 minimum isomers and 30 transition states, is explored theoretically at the B3LYP/6-311G(d,p) and CCSD(T)/6-311G(d,p) (single-point) levels of theory. The initial association between 1CHF and NO2 is found to be the carbon-to-middle-nitrogen attack forming an energy-rich adduct a (HFCNO2) with no barrier, followed by concerted O-shift and C--N bond rupture leading to product P2 (NO + HFCO), which is the most abundant. In addition, a can take a 1,3-H-shift to isomer b (FCN(O)OH) followed by the dissociation to form the second feasible product P4 (OH + FCNO). The least favorable pathway is that b undergoes a concerted OH-shift to form d (HO(F)CNO), which will dissociate to product P5 (HF+OCNO) via side HF-elimination. The secondary dissociation of P5 may form product P7 (HF+NO+CO) easily. Furthermore, the 1CHF attack at the end-O of NO2 is a barrier-consumed process, and thus may only be of significance at high temperatures. The comparison with the analogous reactions 1CHCl + NO2 is discussed. The present study may be helpful for probing the mechanism of the title reaction and understanding the halogenated carbine chemistry.

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PubMed2004

Molecular simulation studies of a selenium-containing scFv catalytic antibody that mimics glutathione peroxidase.

GPX is a mammalian antioxidant selenoenzyme which protects biomembranes and other cellular components from oxidative damage by catalyzing the reduction of a variety of hydroperoxides (ROOH), using Glutathione (GSH) as the reducing substrate. The single-chain Fv fragment of the monoclonal antibody 2F3 (scFv2F3) can be converted into the selenium-containing Se-scFv2F3 by chemical modification of the serine. The new selenium-containing catalytic antibody Se-scFv2F3 acts as a glutathione peroxidase (GPX) mimic with high catalytic efficiency. In order to investigate which residue of scFv2F3 is converted into selenocysteine and to describe the proper reaction site of GSH to Se-scFv2F3, a three-dimensional structure of scFv2F3 is built by means of homology modeling. The 3D model is assessed by molecular dynamics (MD) simulation to determine its stability and by comparison with those of known protein structures. After the serine in the scFv2F3 is modified to selenocysteine, a catalytic antibody (abzyme) is obtained. From geometrical considerations, the solvent-accessible surface of the protein is examined. The computer-aided docking and energy minimization (EM) calculations of the abzyme-GSH complex are then carried out to explore the possible active site of the glutathione peroxidase mimic Se-scFv2F3. The structural information from the theoretically modeled complex can help us to further understand the catalytic mechanism of GPX.

Amino Acid Sequence↗

PubMed2004

Theoretical study on the mechanism of the 1CHCl + NO2 reactions.

The radical-molecule reaction mechanism of (1)CHCl with NO(2) has been explored theoretically at the B3LYP/6-311G(d, p) and CCSD(T)/6-311G(d, p) (single-point) levels of theory. Thirteen minimum isomers and 29 transition states are located. The initial association between (1)CHCl and NO(2) proceeds most likely through the carbon-to-middle-nitrogen attack leading to an energy-rich adduct a (HClCNO(2)), which is found to be a barrierless process. Staring from a, the most feasible channel is to undergo a concerted O-shift and C--N bond rupture leading to product P(2) (NO + HClCO). The minor product pathways are the direct O-extrusion of a to P(3) (O + HClCNO-cis) as well as the 1,3-H-shift of a to isomer b (ClCNOOH) followed by a concerted OH-shift leading to d (HOClCNO), which will dissociate to product P(8) (NO + ClCOH) via C--N cleavage. Because the transition states and isomers involved in the most feasible channel all lie below the reactants, the title reaction is expected to be rapid, as is consistent with the measured rate constant at 296 K. The comparison with the analogous reactions (3)CH(2) + NO(2) are discussed. The present study may be useful for further experimental investigation of the title reaction.

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PubMed2004

Metallophilic attractions between d8-d10 heterometallic compounds trans-[Pt(PH3)2(CN)2] and M(PH3)2+ (M=Ag or Cu): Ab initio study.

The weak metal-metal interactions of Pt(II)-Ag(I)/Cu(I) have been investigated by ab initio method at MP2 level through the model complexes [trans-Pt(PH3)2(CN)2-M(PH3)2+] (M=Ag,Cu). The calculated interaction energy of 12.9 and 11.5 kcal mol(-1) for [trans-Pt(PH3)2(CN)2-Ag(PH3)2+] and [trans-Pt(PH3)2(CN)2-Cu(PH3)2+] respectively, are in the middle of the van der Waals force and the strong hydrogen bond. The estimated equilibrium separations between Pt and M, r(eq)(Pt-M) (3.32 A for M=Ag and 3.23 A for M=Cu), lie within the region expected for weak metal-metal interaction. The electronic dispersive contributions dominate the weak interaction.

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PubMed2004

Theoretical studies on dynamics and thermochemistry of the reactions CF(3)CHCl(2)+Cl-->CF(3)CCl(2)+HCl and CF(3)CHFCl+Cl-->CF(3)CFCl+HCl.

A dual-level direct dynamics study has been carried out for the two hydrogen abstraction reactions CF(3)CHCl(2)+Cl and CF(3)CHFCl+Cl. The geometries and frequencies of the stationary points are optimized at the BHLYP/6-311G(d,p), B3LYP/6-311G(d,p), and MP2/6-31G(d) levels, respectively, with single-point calculations for energy at the BHLYP/6-311++G(3df,2p), G3(MP2), and QCISD(T)/6-311G(d,p) levels. The enthalpies of formation for the species CF(3)CHCl(2), CF(3)CHFCl, CF(3)CCl(2), and CF(3)CFCl are evaluated at higher levels. With the information of the potential energy surface at BHLYP/6-311++G(3df,2p)//6-311G(d,p) level, we employ canonical variational transition-state theory with small-curvature tunneling correction to calculate the rate constants. The agreement between theoretical and experimental rate constants is good in the measured temperature range 276-382 K. The effect of fluorine substitution on reactivity of the C-H bond is discussed.

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PubMed2004

Density functional investigation of reaction of borohydride cation BH2+ with propylene.

The reactions of BH2+ with propylene (CH2=CHCH3) to form both the adducts BC3H8+ and the H2-elimination products BC3H6+ + H2 have been investigated at the density functional B3LYP/6-311G(d,p) level of theory. It is shown that the electrophilic attacks of BH2+ towards two olefinic carbons of H2C=CHCH3 and two subsequent 1,3-H-shifts may form four low-lying BC3H8+ isomers (with the relative energies in parentheses in kcal/mol): 1 BH2+.CH2CHCH3 (0.0), 1' BH2+.CH3CHCH2 (6.3), 3 BHCH2CH2CH3+ (4.3), and 4 BHCH(CH3)2+ (5.0), respectively. On the other hand, further H2-eliminations may also occur easily between B-C bonds of isomers 1 and 1' and between C-C bonds of isomers 3 and 4 to form two dissociation products (P1) HBCHCHCH3+ + H2 and (P2) HBC(CH3)CH2+ + H2, with H2-elimination from isomer 1 to be energetically most favorable. According to our calculated mechanism, the collisional stabilization processes of low-lying isomers 1, 1', 3, and 4 may compete extensively with their H2-eliminations processes for the title reaction, leading mainly to some linear carborane cations. This study may be helpful for understanding the stereochemical aspects of borohydride cations towards alkylenes.

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PubMed2004

Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl.

The multiple channel reaction H + CH(3)CH(2)Cl --> products has been studied by the ab initio direct dynamics method. The potential energy surface information is calculated at the MP2/6-311G(d,p) level of theory. The energies along the minimum energy path are further improved by single-point energy calculations at the PMP4(SDTQ)/6-311+G(3df,2p) level of theory. For the reaction, four reaction channels (one chlorine abstraction, one alpha-hydrogen abstraction, and two beta-hydrogen abstractions) have been identified. The rate constants for each reaction channel are calculated by using canonical variational transition state theory incorporating the small-curvature tunneling correction in the temperature range 298-5000 K. The total rate constants, which are calculated from the sum of the individual rate constants, are in good agreement with the experimental data. The calculated temperature dependence of the branching fractions indicates that for the title reaction, H-abstraction reaction is the major reaction channel in the whole temperature range 298-5000 K.

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PubMed2004

Theoretical study on the rate constants for the C2H5 + HBr --> C2H6 + Br reaction.

The reaction C(2)H(5) + HBr --> C(2)H(6) + Br has been theoretically studied over the temperature range from 200 to 1400 K. The electronic structure information is calculated at the BHLYP/6-311+G(d,p) and QCISD/6-31+G(d) levels. With the aid of intrinsic reaction coordinate theory, the minimum energy paths (MEPs) are obtained at the both levels, and the energies along the MEP are further refined by performing the single-point calculations at the PMP4(SDTQ)/6-311+G(3df,2p)//BHLYP and QCISD(T)/6-311++G(2df,2pd)//QCISD levels. The calculated ICVT/SCT rate constants are in good agreement with available experimental values, and the calculate results further indicate that the C(2)H(5) + HBr reaction has negative temperature dependence at T < 850 K, but clearly shows positive temperature dependence at T > 850 K. The current work predicts that the kinetic isotope effect for the title reaction is inverse in the temperature range from 200 to 482 K, i.e., k(HBr)/k(DBr) < 1.

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PubMed2004

Direct ab initio dynamics studies on the hydrogen-abstraction reactions of OH radicals with HOX (X = F, Cl, and Br).

The hydrogen abstract reactions of OH radicals with HOF (R1), HOCl (R2), and HOBr (R3) have been studied systematically by a dual-level direct-dynamics method. The geometries and frequencies of all the stationary points are optimized at the MP2/6-311+G(2d, 2p) level of theory. A hydrogen-bonded complex is located at the product channel for the OH + HOBr reaction. To improve the energetics information along the minimum energy path (MEP), single-point energy calculations are carried out at the CCSD(T)/6-311++G(3df, 3pd) level of theory. Interpolated single-point energy (ISPE) method is employed to correct the energy profiles for the three reactions. It is found that neither the barrier heights (DeltaE) nor the H-O bond dissociation energies [D(H-O)] exhibit any clear-cut linear correlations with the halogen electronegative. The decrease of DeltaE and D(H-O) for the three reactions are in order of HOF > HOBr > HOCl. Rate constants for each reaction are calculated by canonical variational transition-state theory (CVT) with a small-curvature tunneling correction (SCT) within 200-2000 K. The agreement of the rate constants with available experimental values for reactions R2 and R3 at 298 K is good. Our results show that the variational effect is small while the tunneling correction has an important contribution in the calculation of rate constants in the low-temperature range. Due to the lack of the kinetic data of these reactions, the present theoretical results are expected to be useful and reasonable to estimate the dynamical properties of these reactions over a wide temperature range where no experimental value is available.

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PubMed2004

Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase.

Although the GSK3/SHAGGY-like kinase is a highly conserved serine/threonine kinase implicated in many signaling pathways in eukaryotes, the lack of knowledge of its three-dimensional (3D) structure has hindered efforts to understand the binding specificities of substrate and catalytic mechanism. To understand the structure-activity relationships, the protein 3D structure was built by using homology modeling based on the known X-ray diffraction structure of Glycogen synthase kinase-3beta (Gsk3beta) and the model structure was further refined using unrestrained molecular dynamics simulations. The research indicates that the general 3D organization of the GSK3/SHAGGY-like kinase is a typical kinase family and comprises an N-terminal domain of beta-sheet and a larger C-terminal domain mainly constituted by alpha-helix. In order to understand the molecular interactions between the natural substrate-ATP and GSK3/SHAGGY-like kinase, a 3D model of the complex ATP-GSK3/SHAGGY-like kinase is developed by molecular docking program, which is helpful to guide the experimental realization and the new mutant designs as well. One important finding is that the identification of the key binding-site residue of Lys69 which plays an important role in the catalysis of GSK3/SHAGGY-like kinase and this is in consistent with experimental observation.

Adenosine Triphosphate↗

PubMed2003

Insect resistance conferred by 283-kDa Photorhabdus luminescens protein TcdA in Arabidopsis thaliana.

The tcdA gene of Photorhabdus luminescens encodes a 283-kDa protein, toxin A, that is highly toxic to a variety of insects, including some agriculturally important pests. We tested the efficacy of transgenic toxin A in Arabidopsis thaliana for control of feeding insects. Plants with toxin A expression above about 700 ng/mg of extractable protein were highly toxic to tobacco hornworm (Manduca sexta). Toxin A isolated from transgenic plants also strongly inhibited growth of the southern corn rootworm (Diabrotica undecimpunctata howardi). Addition of 5' and 3' untranslated regions of a tobacco osmotin gene (osm) increased toxin A production 10-fold and recovery of insect-resistant lines 12-fold. In the best line, high toxin A expression and insect resistance were maintained for at least five generations in all progeny. The intact tcdA mRNA represents the largest effective transgenic transcript produced in plants to date. These results may open a new route to transgenic pest control in agriculture.

Animals↗

PubMed2003

Dual-level direct dynamics studies for the reactions of dimethyl ether with hydrogen atom and methyl radical.

The dual-level direct dynamics approach is employed to study the dynamics of the CH(3)OCH(3) + H (R1) and CH(3)OCH(3) + CH(3) (R2) reactions. Low-level calculations of the potential energy surface are carried out at the MP2/6-311+G(d,p) level of theory. High-level energetic information is obtained at the QCISD(T) level of theory with the 6-311+G(3df,3pd) basis set. The dynamics calculations are performed using variational transition state theory (VTST) with the interpolated single-point energies (ISPE) method, and small-curvature tunneling (SCT) is included. It is shown that the reaction of CH(3)OCH(3) with H (R1) may proceed much easier and with a lower barrier height than the reaction with CH(3) radical (R2). The calculated rate constants and activation energies are in good agreement with the experimental values. The calculated rate constants are fitted to k(R1) = 1.16 x 10(-19) T(3) exp(-1922/T) and k(R2) = 1.66 x 10(-28) T(5) exp(-3086/T) cm(3) mol(-1) s(-1) over a temperature range 207-2100 K. Furthermore, a small variational effect and large tunneling effect in the lower temperature range are found for the two reactions.

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PubMed2002

DFT and ab initio direct dynamics studies on the hydrogen abstraction reactions of chlorine atoms with CH(4-n)F(n) (n = 1-3).

A direct dynamics study is carried out for the hydrogen abstraction reactions Cl + CH(4-n)F(n) (n = 1-3) in the temperature range of 200-1,000 K. The minimum energy paths (MEPs) of these reactions are calculated at the BH&H-LYP/6-311G(d,p) level, and the energies along the MEPs are further refined at the QCISD(T)/6-311+G(2df,2p) and QCISD(T)/6-311+G(d,p) (single-point) level. The rate constants obtained by using the improved canonical variational transition state theory incorporating small-curvature tunneling correction (ICVT/SCT) are in good agreement with the available experimental results. It is shown that the vibrational adiabatic potential energy curves for these reactions have two barriers, a situation similar to the analogous reactions CH(3)X+Cl (X=Cl, Br). The theoretical results show that for the title reactions the variational effect should not be neglected over the whole considered temperature range, while the small-curvature tunneling effect is only important in the lower temperature range. The effects of fluorine substitution on the rate of this kind of reactions are also examined.

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