Biomedical subjects

Ze-Sheng Li

Publications and source records attributed to Ze-Sheng Li.

At least 19 recordsLinked to original sources

PubMed2007

Molecular dynamics simulation study on controlling the adsorption behavior of polyethylene by fine tuning the surface nanodecoration of graphite.

Molecular dynamics simulations are applied to study the adsorption of polyethylene with different chain lengths on patterned graphite surfaces that contain nanoscale protrusions. The influence of the nanostructure on the strong attractive interaction inherently in the hydrophobic polyethylene and hydrophobic graphite system is investigated by modifying the top surface area and the height and the shape of the protrusions. The results are analyzed in terms of the chain configuration, the adsorption energy, the global orientational order parameter, and the normalized surface-chain contacting pair number in the first adsorption layer. When the size of the protrusion increases, the adsorption energy, the order parameter, and the normalized surface-chain contacting pair number decrease at a fixed chain length. When the size of the protrusion is fixed, the average adsorption energy per monomer and the order parameter decrease with increasing chain length because of the stronger intramolecular interactions between the monomers. Changing the protrusion shape in a suitable way will effectively reduce the strong surface-chain interaction.

Journal Article↗

PubMed2007

Theoretical study and rate constant calculation for reaction of CF(3)CH(2)OH with OH.

The reaction mechanism of CF(3)CH(2)OH with OH is investigated theoretically and the rate constants are calculated by direct dynamics method. The potential energy surface (PES) information, which is necessary for dynamics calculation, is obtained at the B3LYP/6-311G (d, p) level. The single-point energy calculations are performed at the MC-QCISD level using the B3LYP geometries. Complexes, with the energies being less than corresponding reactants and products, are found at the entrance and exit channels for methylene-H-abstraction channel, while for the hydroxyl-H-abstraction channel only entrance complex is located. By means of isodesmic reactions, the enthalpies of the formation for the species CF(3)CH(2)OH, CF(3)CHOH, and CF(3)CH(2)O are estimated at the MC-QCISD//B3LYP/6-311G (d, p) level of theory. The rate constants for two kinds of H-abstraction channels are evaluated by canonical variational transition state theory with the small-curvature tunneling correction (CVT/SCT) over a wide range of temperature 200-2000 K. The calculated results are in good agreement with the experimental values in the temperature region 250-430 K. The present results indicate that the two channels are competitive. Below 289 K, hydroxyl-H-abstraction channel has more contribution to the total rate constants than methylene-H-abstraction channel, while above 289 K, methylene-H-abstraction channel becomes more important and then becomes the major reaction channel.

Journal Article↗

PubMed2006

An automatic coarse-graining and fine-graining simulation method: application on polyethylene.

Multiscale modeling of a polymeric system is a challenging task in polymer physics. Here we introduce a bottom-up and then top-down scheme for the simulation of polyethylene (PE). The coarse-grained numerical potential for PE is derived through an automatic updating program by mapping its radial distribution function (RDF) from the Lowe-Andersen temperature controlling (LA) simulation onto the one from detailed molecular dynamics (MD) simulation. This coarse-grained numerical potential can be applied in larger systems under the same thermodynamic conditions. We have tested the reliability of the derived potential in two ways. First, the blends of different linear low-density polyethylene (LLDPE) with high-density polyethylene (HDPE) have been simulated in LA with the coarse-grained numerical potentials and reasonable results are obtained. Moreover, Rouse scaling behavior is reproduced for monodispersed polymeric systems with different chain lengths. The atomistic details of the beads can be reintroduced into the coarse-grained HDPE and LLDPE/HDPE models, followed by a few MD runs to alleviate the local tension induced by this fine-graining procedure. The equilibrated large atomistic system can then be used for further studies.

Journal Article↗

PubMed2006

Dissipative particle dynamics study on the morphology changes of diblock copolymer lamellar microdomains due to steady shear.

The morphology changes of linear diblock copolymer lamellar microdomains under uniform simple shear are studied via the dissipative particle dynamics technique. The parallel and perpendicular reorientations of the lamellae are observed in the simulations, and two different reorientation mechanisms, under small and large shear rates respectively, are proposed. The parallel-to-perpendicular transition is also observed and the kinetics is discussed. Sinusoidal and chevron instabilities due to the shear are found. After relaxation the peculiar "bidirectionally undulating" instability is obtained.

Journal Article↗

PubMed2006

Direct dynamics study on hydrogen abstraction reaction of CF3CF2CH2OH with OH radical.

The dual-level direct dynamics method has been employed to investigate the H-abstraction reaction of CF(3)CF(2)CH(2)OH with OH radical, which is predicted to have two classes of possible reaction channels caused by different positions of hydrogen atom attack. The minimum-energy path is calculated at the B3LYP/6-311G(d,p) level, and the energetic information is further refined by the MC-QCISD method. To compare the structures, the other method MPW1K/6-311G(d,p) is also applied to this system. Hydrogen-bonded complexes are presented in the reactant and product sides of the three channels, indicating that each reaction may proceed via an indirect mechanism. The rate constants for each reaction channel are evaluated by canonical variational transition-state theory (CVT) with the small-curvature tunneling correction (SCT) over a wide range of temperatures from 200 to 2000 K. The calculated CVT/SCT rate constants are found to be in good agreement with the available experimental values. The result shows that the variational effect is small, and in the lower-temperature range, the SCT effect is important for each reaction. It is shown that hydrogen abstracted from the -CH(2)- position is the major channel, while H-abstraction from the -OH position may be neglected with the temperature increasing.

Journal Article↗

PubMed2006

Theoretical mechanistic study on the radical-molecule reaction of CHCl2/CCl3 with NO2.

The radical-molecule reaction mechanism of CHCl(2) and CCl(3) with NO(2) have been explored theoretically at the B3LYP/6-311G(d,p) and MC-QCISD (single-point) levels. For the singlet potential energy surface (PES) of CHCl(2) + NO(2) reaction, the association of CHCl(2) with NO(2) was found to be a barrierless carbon-to-nitrogen approach forming an energy-rich adduct a (HCl(2)CNO(2)) followed by isomerization to b(1) (trans-cis-HCl(2)CONO), which can easily interconvert to b(2), b(3), and b(4). Subsequently, the most feasible pathway is the 1,3-chlorine migration associated with N-O1 bond cleavage of b(1) leading to P(1) (CHClO + ClNO). The second competitive pathway is the 1,4-chlorine migration along with N-O1 bond rupture of b(4) giving rise to P(2) (CHClO + ClON). Moreover, some of P(1) and P(2) can further dissociate to give P(6) (CHClO + Cl + NO). The lesser followed competitive channel is the 1,3-H-shift from C to N atom along with N-O1 bond rupture of b(1) to form P(3) (CCl(2)O + HNO). The concerted 1,4-H-shift accompanied by N-O1 bond fission of b(3) to product P(4) (CCl(2)O + HON) is even much less feasible. For the singlet PES of CCl(3) + NO(2) reaction, the only primary product is found to be P(1) (CCl(2)O + ClNO), which can lead to P(2) (CCl(2)O + Cl + NO) via dissociation of ClNO. The obtained major products CHClO and CCl(2)O for CHCl(2) + NO(2) and CCl(3) + NO(2) reactions, respectively, are in good agreement with kinetic detection in experiment. Compared with the singlet pathways, the triplet pathways may have less contributions to both reactions. Because the rate-determining transition state involved in the feasible pathways lie above the reactants R, the title reactions may be important in high-temperature processes. The similarities and discrepancies among the CH(n)Cl(3-n) + NO(2) (n == 0-2) reactions are discussed in terms of the substitution effect. The present study may be helpful for further experimental investigation of the title reactions.

Chloroform↗

PubMed2006

Theoretical study of Al(n) and Al(n)O (n = 2-10) clusters.

The stable structures, energies, and electronic properties of neutral, cationic, and anionic clusters of Al(n) (n = 2-10) are studied systematically at the B3LYP/6-311G(2d) level. We find that our optimized structures of Al5(+), Al9(+), Al9(-), Al10, Al10(+), and Al10(-) clusters are more stable than the corresponding ones proposed in previous literature reports. For the studied neutral aluminum clusters, our results show that the stability has an odd/even alternation phenomenon. We also find that the Al3, Al7, Al7(+), and Al7(-) structures are more stable than their neighbors according to their binding energies. For Al7(+) with a special stability, the nucleus-independent chemical shifts and resonance energies are calculated to evaluate its aromaticity. In addition, we present results on hardness, ionization potential, and electron detachment energy. On the basis of the stable structures of the neutral Al(n) (n = 2-10) clusters, the Al(n)O (n = 2-10) clusters are further investigated at the B3LYP/6-311G(2d), and the lowest-energy structures are searched. The structures show that oxygen tends to either be absorbed at the surface of the aluminum clusters or be inserted between Al atoms to form an Al(n-1)OAl motif, of which the Al(n-1) part retains the stable structure of pure aluminum clusters.

Journal Article↗

PubMed2006

Theoretical mechanistic study on the radical-radical reaction of ketenyl with nitrogen dioxide.

The radical-radical reaction between the ketenyl radical (HCCO) and nitrogen dioxide (NO(2)) played a very important role in atmospheric and combustion chemistry. Motivated by recent laboratory characterization about the reaction kinetics of ketenyl radical with nitrogen dioxide, in this contribution, we applied the coupled cluster and density functional theory to explore the mechanism of the title reaction. These calculations indicate that the title reaction proceeds mostly through singlet pathways, less go through triplet pathways. It is found that the HCCO + NO(2) reaction initially favors formation of adduct OCCHNO(2) (1) with no barrier. Subsequently, starting from isomer 1, the most feasible pathway is ring closure of 1 to isomer O-cCCHN(O)O (2) followed by CO(2) extrusion to product HCNO + CO(2) (P(1)), which is the major product with predominant yields. Much less competitively, 1 can take the successive 1,3-H- and 1,3-OH-shift interconversion to isomer OCCNOHO (3(a), 3(b), 3(c)) and then to isomer OCOHCNO (4(a), 4(b)), which can finally take a concerted H-shift and C-C bond fission to give HCNO + CO(2) (P(1)). The least competitive pathway is the ring-closure of isomer 3(a) to form isomer O-cCCN(OH)O (5(a), 5(b)) followed by dissociation to HONC + CO(2) (P(2)) through the direct side CO(2) elimination. Because the intermediates and transition states involved in the most favorable channel all lie below the reactants, the title reaction is expected to be rapid, as is confirmed by experiment. Therefore, it can be significant for elimination of nitrogen dioxide pollutants. The present results can lead us to a deep understanding of the mechanism of the title reaction and can be helpful for understanding NO(x)-combustion chemistry.

Journal Article↗

PubMed2006

The dependence of nanostructures on the molecule rigidity of A2(B4)2-type miktoarm block copolymer.

Using the dissipative particle dynamics simulation technique, we have studied the influence of the molecule rigidity on the nanostructures of the A2(B4)2-type miktoarm block copolymers. A typical spherical micellar ordered structure is obtained for a coil-coil miktoarm block copolymer in melt. By introducing a bond angle potential in our model to enhance the molecule rigidity systematically, we find, respectively, a hexagonal cylindrical structure and a parallel ellipsoid in lamellae structure which is discovered for the first time.

Journal Article↗

PubMed2006

Theoretical study on the mechanism of the CH2F + NO2 reaction.

Despite the importance of the Fluoromethyl radicals in combustion chemistry, very little experimental information on their reactions toward stable molecules is available in the literature. Motivated by recent laboratory characterization about the reaction kinetics of Chloromethyl radicals with NO2, we carried out a detailed potential energy survey on the CH2F + NO2 reaction at the B3LYP/6-311G(d,p) and MC-QCISD (single-point) levels as an attempt toward understanding the CH2F + NO2 reaction mechanism. It is shown that the CH2F radical can react with NO2 to barrierlessly generate adduct a (H2FCNO2), followed by isomerization to b1 (H2FCONO-trans) which can easily interconvert to b2 (H2FCONO-cis). Subsequently, Starting from b (b1, b2), the most feasible pathway is the C--F and N--O1 bonds cleavage along with N--F bond formation of b (b1, b2) leading to P1 (CH2O + FNO), or the direct N--O1 weak-bond fission of b (b1, b2) to give P2 (CH2FO + NO), or the 1,3-H-shift associated with N--O1 bond rupture of b1 to form P3 (CHFO + HNO), all of which may have comparable contribution to the reaction CH2F + NO2. Much less competitively, b2 either take the 1,4-H-shift and O1--N bond cleavage to form product P4 (CHFO + HON) or undergo a concerted H-shift to isomer c2 (HFCONOH), followed by dissociation to P4. Because the rate-determining transition state (TSab1) in the most competitive channels is only 0.3 kcal/mol higher than the reactants in energy, the CH2F + NO2 reaction is expected to be rapid, and may thus be expected to significantly contribute to elimination of nitrogen dioxide pollutants. The similarities and discrepancies among the CH2X + NO2 (X = H, F, and Cl) reactions are discussed in terms of the electronegativity of halogen atom. The present article may assist in future experimental identification of the product distributions for the title reaction, and may be helpful for understanding the halogenated methyl chemistry.

Journal Article↗

PubMed2005

A molecular-dynamics simulation study of diffusion of a single model carbonic chain on a graphite (001) surface.

Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the solid-liquid interface. Furthermore, we have studied the relation between the mean-square gyration radius and N. [Figure: see text].

Carbon↗

PubMed2005

DFT and ab initio dual-level direct dynamics studies on the reactions of fluorine atom with HOCl and HOBr.

The multichannel reactions (1) HOCl + F --> products and (2) HOBr + F --> products have been investigated using the dual-level direct dynamics method. The minimum energy paths (MEPs) are calculated at both the MPW1K/6-311G(d,p) and QCISD/6-311G(d,p) levels, then the single-point energies are further corrected at the QCISD(T)/6-311++G(3df,3pd) level of theory. There are hydrogen-bonded complexes with the energies less than those of the reactants or products located at the entrance or exit channel of both hydrogen abstraction reactions; while for the halogen abstraction channels only one complex exists at the reactant side in the bromine abstraction channel. The rate constants are evaluated by the improved canonical variational transition-state theory (ICVT). The agreement of the rate constants with available experimental values for two reactions at room temperature is good. Theoretical results indicate that for the reaction HOCl + F, hydrogen abstraction channel leading to the formation of HF + ClO will predominate the reaction over the whole temperature range, and the reaction of HOBr + F may proceed mainly through the bromine abstraction channel at the lower temperature while the contribution of hydrogen abstraction channel will become significant as the temperature increases. Because of 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.

Journal Article↗

PubMed2005

Molecular dynamics simulation study on adsorption and diffusion processes of a hydrophilic chain on a hydrophobic surface.

Molecular dynamics simulations are applied to investigate the adsorption and diffusion processes of a single hydrophilic poly(vinyl alcohol) (PVA) chain with different chain lengths on a hydrophobic graphite surface. It is expected that the chain and the surface "dislike" each other because one is hydrophilic and the other is hydrophobic. But surprisingly, a short PVA chain is well adsorbed on the surface, accompanied by large changes in the chain configuration. With increasing degree of polymerization (N), the chain turns gradually from two-dimensional adsorption to possessing certain height in the direction perpendicular to the surface. Moreover, the adsorption energy increases and the diffusion coefficient decreases with increasing N. In particular, for N = 20 in equilibrium, the hydroxyls of this short chain are close to the graphite surface in the stable adsorption configuration. In addition, we change the effective dielectric constant to 76.0 to mimic good solvent condition. The chain configurations and the diffusion coefficients both vary in contrast to the foregoing results.

Journal Article↗

PubMed2005

Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8.

With homology modeling techniques, molecular mechanics, and molecular dynamics methods, a 3D structure model of Ndx1 is created and refined. This model is further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed and the result indicates that Glu46, Arg88, and Glu90 are three important determinant residues in binding, as they have strong hydrogen bonding interactions and electrostatic interactions with Ap6A. In addition, we further find that three residues, Ser38, Leu39 and Glu46, coordinate enzyme-bound Mg2+ ions in complex N-A. The Glu46 is consistent with the experimental results by Iwai et al., and the other four residues mentioned above may also play vital roles in catalysis of Ndx1.

Amino Acid Sequence↗

PubMed2005

Dissipative particle dynamics study on the interfaces in incompatible A/B homopolymer blends and with their block copolymers.

Dissipative particle dynamics, a simulation technique appropriate at mesoscopic scales, has been applied to investigate the interfaces in immiscible binary A/B homopolymer blends and in the ternary systems with their block copolymers. For the binary blends, the interfacial tension increases and the interface thickness decreases with increasing Flory-Huggins interaction parameter chi while the homopolymer chain length is fixed. However, when the chi parameter and one of the homopolymer chain length is fixed, increasing another homopolymer chain length will induce only a small increase on interfacial tension and slight decrease on interface thickness. For the ternary blends, adding the A-b-B block copolymer will reduce the interfacial tension. When the mole number of the block copolymer is fixed, longer block chains have higher efficiency on reducing the interfacial tension than the shorter ones. But for the block copolymers with fixed volume fraction, shorter chains will be more efficient than the longer ones on reducing the interfacial tension. Increasing the block copolymer concentration reduces interfacial tension. This effect is more prominent for shorter block copolymer chains.

Journal Article↗

PubMed2005

Theoretical study for the reaction of CH3OCl with Cl atom.

A direct dynamics method is employed to study the kinetics of the multiple channel reaction CH(3)OCl + Cl. The potential energy surface (PES) information is explored from ab initio calculations. Two reaction channels, Cl- and H-abstractions, have been identified. The optimized geometries and frequencies of the stationary points and the minimum-energy paths (MEPs) are calculated at the MP2 level of theory using the 6-311G(d, p) and cc-pVTZ basis sets, respectively. The single-point energies along the MEPs are further refined at the G3(MP2)//MP2/6-311G(d, p), G3//MP2/6-311G(d, p), as well as by the multicoefficient correlation method based on QCISD (MC-QCISD) using the MP2/cc-pVTZ geometries. The enthalpies of formation for the species CH(3)OCl and CH(2)OCl are calculated via isodesmic reactions. The rate constants of the two reaction channels are evaluated by using the variational transition-state theory over a wide range of temperature, 220-2200 K. The calculated rate constants exhibit the slightly negative temperature dependence and show good agreement with the available experimental data at room temperature at the G3(MP2)//MP2/6-311G(d, p) level. The present calculations indicate that the two channels are competitive at low temperatures while H-abstraction plays a more important role with the increase of temperature. The calculated k(1a)/k(1) ratio of 0.5 at 298 K is in general agreement with the experimental one, 0.8 +/- 0.2. The high rate constant for CH(3)OCl + Cl shows that removal by reaction with Cl atom is a potentially important loss process for CH(3)OCl in the polar stratosphere.

Journal Article↗

PubMed2005

Stability of two-dimensional tessellation ice on the hydroxylated beta-cristobalite (100) surface.

Monolayer adsorbed water on the beta-cristobalite (100) surface is studied via classical molecular dynamics simulations. The ordered two-dimensional (2D) tessellation ice structure (i.e., the four-membered and the eight-membered rings appear alternatively) is justified at low temperatures in the simulations. The stability of this possible new ice phase is further investigated by heating the system from 5 to 300 K. An order-disorder structural transition is observed between 100 and 200 K, featuring the melting process of the tessellation ice. This process is characterized by the water oxygen-oxygen radial distribution function, the coordination number, the distance vector between the center of mass of the oxygen and the hydrogen atoms in water, the mean square displacement of oxygen in water, and the vibrational density of state. The above techniques show consistency on that the order-disorder transition temperature of the 2D tessellation ice is far below 300 K. The 2D tessellation ice structure is also obtained via density functional calculations with different generalized gradient approximations. By comparing the calculated adsorption and the lateral energies between different methods, we find that the melting temperature of the specific 2D ice structure is strongly method dependent. Therefore, further experimental works are urged to justify this possible new ice phase and probe its stability.

Computer Simulation↗

PubMed2005

Homology modeling and PAPS ligand (cofactor) binding study of bovine phenol sulfotransferase.

In order to understand the mechanisms of ligand binding and the interaction between the ligand and the bovine phenol sulfotransferase, (bSULT1A1, EC 2.8.2.1) a three-dimensional (3D) model of the bSULT1A1 is generated based on the crystal structure of the estrogen sulfotransferase (PDB code 1AQU) by using the InsightII/Homology module. With the aid of the molecular mechanics and molecular dynamics methods, the final refined model is obtained and is further assessed by Profile-3D and ProStat, which show that the refined model is reliable. With this model, a flexible docking study is performed and the results indicate that 3'-phosphoadenosine-5'- phosphosulfate (PAPS) is a more preferred ligand than coenzyme A (CoA), and that His108 forms hydrogen bond with PAPS, which is in good agreement with the experimental results. From these docking studies, we also suggest that Phe255, Phe24 and Tyr169 in bSULT1A1 are three important determinant residues in binding as they have strong van-der-Waals contacts with the ligand. The hydrogen-bonding interactions also play an important role for the stability of the complex. Our results may be helpful for further experimental investigations.

Amino Acid Sequence↗