Chia-Chung Sun

Jilin University, Jilin, Jilin Sheng, China

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Publications (447)944.28 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: We use multibody dissipative particle dynamics method, which can effectively consider the attractive and repulsive interactions, to investigate evaporation-induced morphology patterns of triblock copolymers A5B10C5 in thin films. With changing attractive interactions between solvent vapor and triblock copolymers that represent various selective solvents, lamellar morphology perpendicular to the surface, sandwich lamellar morphology parallel to the surface, spherical morphology and disorder morphology pattern of thin films are obtained, for both Coil-Coil-Coil and Rod-Coil-Coil chain architectures, respectively. The order parameter and the film thickness are calculated during the process for characterizing the film properties, and we find rigid A-block of the triblock copolymers hinders the formation of ordered structure.
    Chemical Research in Chinese Universities 01/2014; 30(1):144 —148. · 0.74 Impact Factor
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    ABSTRACT: We study the self-assembly behaviour of two-patch particles with D ∞h symmetry by using Brownian dynamics simulations. The self-assembly process of two-patch particles with diverse patch coverage in two selective solvent conditions is investigated. The patchy particles in a solvent that is bad for patches but good for matrix form linear thread-like structures with low patch coverage, whereas they form 3D network structures with relatively high patch coverage on surface. For patchy particles in a solvent which is good for patches but bad for body, monolayer structures are obtained at high patch coverage, and some cluster structures emerge when surface patch coverage is low.
    Molecular Simulation 01/2014; 40(6):449-457. · 1.06 Impact Factor
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    ABSTRACT: How to generate a non-zero first hyperpolarizability for a centrosymmetric molecule is a challenging question. In this paper, an external (pump) electric field is used to make a centrosymmetric benzene molecule generate a non-zero value of the electric field induced first hyperpolarizability (β (F) ). This comes from the centrosymmetry breaking of electron cloud. Two interesting rules are exhibited. (1) β (F) is anisotropic for different directional fields (F i, i = X, Y, Z). (2) The field dependence of β (F) is a non-monotonic function, and an optimum external electric field causes the maximum value of β (F) . The largest first hyperpolarizability β (F) reaches the considerable level of 3.9 × 10(5) a.u. under F Y = 330 × 10(-4) a.u. for benzene. The external electric field effects on non-centrosymmetric edge-modified graphene ribbon H2N-(3,3)ZGNR-NO2 was also studied in this work. The first hyperpolarizability reaches as much as 2.1 × 10(7) a.u. under F X = 600 × 10(-4) a.u. for H2N-(3,3)ZGNR-NO2. We show that the external electric field can not only create a non-zero first hyperpolarizability for centrosymmetric molecule, but also remarkably enhance the first hyperpolarizability for a non-centrosymmetric molecule.
    Journal of Molecular Modeling 07/2013; · 1.98 Impact Factor
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    ABSTRACT: The C-terminus tail (G144-T149) of the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) plays an important role in this protein's hyperstabilization and may therefore be a good protein stability tag. Detailed understanding of the structural and dynamic effects of C-terminus tail deletion is required for gaining insights into the thermal stability mechanism of Sto-RNase HI. Focused on Sulfolobus tokodaii RNase HI (Sto-RNase HI) and its derivative lacking the C-terminal tail (ΔC6 Sto-RNase HI) (PDB codes: 2EHG and 3ALY), we applied molecular dynamics (MD) simulations at four different temperatures (300, 375, 475, and 500 K) to examine the effect of the C-terminal tail on the hyperstabilization of Sto-RNase HI and to investigate the unfolding process of Sto-RNase HI and ΔC6 Sto-RNase HI. The simulations suggest that the C-terminal tail has significant impact in hyperstabilization of Sto-RNase HI and the unfolding of these two proteins evolves along dissimilar pathways. Essential dynamics analysis indicates that the essential subspaces of the two proteins at different temperatures are non-overlapping within the trajectories and they exhibit different directions of motion. Our work can give important information to understand the three-state folding mechanism of Sto-RNase HI and to offer alternative strategies to improve the protein stability.
    Journal of Molecular Modeling 03/2013; · 1.98 Impact Factor
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    ABSTRACT: Using the strong electron hole cage C20F19 acceptor, the NH2…M/M3O (M = Li, Na, and K) complicated donors with excess electron and the unusual σ chain (CH2)4 bridge, we construct a new kind of electride molecular salts e-@C20F19-(CH2)4-NH2…M+/M3O+ (M = Li, Na, and K) with excess electron anion inside the hole cage (to be encapsulated excess electron-hole pair) serving as a new A-B-D strategy for enhancing nonlinear optical (NLO) response. An interesting push-pull mechanism of excess electron generation and its long range transfer is exhibited. The excess electron is pushed out from the (super)alkali atom M/M3O by the lone pair of NH2 in the donor and further pulled to inside the hole cage C20F19 acceptor through the efficient long σ chain (CH2)4 bridge. Owing to the long range electron transfer, the new designed electride molecular salts with the excess electron-hole pair exhibit large NLO response. For the e-@C20F19-(CH2)4-NH2…Na+, its large first hyperpolarizability (β0) reaches up to 9.5×106 a.u. which is about 2.4×104 times of 400 a.u. for the relative e-@C20F20…Na+ without the extended chain (CH2)4-NH2.1 It is shown that the new strategy is considerably efficient in enhancing the NLO response for the salts. In addition, the effects of different bridges and alkali atomic number on β0 are also exhibited. Further, three modulating factors are found for enhancing NLO response. They are the σ chain bridge, bridge-end group with lone pair and (super)alkali atom. The new knowledge may be significant for designing new NLO materials and electronic devices with electrons inside the cages. They may also be the basis of establishing potential organic chemistry with electron-hole pair.
    The Journal of Physical Chemistry A 03/2013; · 2.77 Impact Factor
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    ABSTRACT: Triazatruxene derivatives and heterofluorenes have drawn increasing attention in the applications of OLED devices due to their particular electronic structures and optical properties. To improve on the thermal and morphological stability and enhance electroluminescent (EL) efficiency, six series of star-shaped triazatruxene/heterofluorene co-polymers have been designed. To reveal structure–property relationships of the novel functional materials, an in-depth theoretical investigation was elaborated using the density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The results HOMOs, LUMOs, ΔH–L, Eg, as well as some other electronic structures and IPs, EAs, λ, τ, the absorption and emission spectra can be tuned by the introduction of heterofluorenes into the triazatruxene core. The various properties of these co-polymers were obtained by extrapolating those of the co-oligomers to infinite chain length. It was concluded that these triazatruxene/heterofluorene co-polymers are interesting optoelectronic functional materials, which have great potential for the application in OLEDs.
    Dyes and Pigments 02/2013; 96(2):349–363. · 3.53 Impact Factor
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    ABSTRACT: The Pi-class GST enzyme (GSTP1) has been extensively studied because of its potential role in disease research. However, a detailed understanding of human GSTP1*D requires an accurate structure, which has not been determined yet. We constructed a high-quality model structure of human GSTP1*D by molecular dynamics simulations and revealed the interactions between the proteins and five inhibitors including chlorambucil, ethacrynic acid, EA-glutathione conjugation and CBL-glutathione conjugation to explore the structure–function relationship. We identified several critical residues, including Phe8, Arg13, Val35, Ile104, Tyr108 and Val113. Our results revealed the specific selectivity of Phe8 and Tyr108 to the substrate. And we provied a new explanation for how does Ile104 influence the substrate binding and a hypothesis about the indirect interaction between Val113 and Tyr108. These results may illustrate the alteration of enzymatic activity in the variants of GSTP1. In addition, the influence of glutathione conjugate on ligands was observed. This work will be a good starting point for further determination of the biological role and structure-based inhibitor design of human Pi-class GST.
    Molecular Simulation 01/2013; 39(7). · 1.06 Impact Factor
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    ABSTRACT: Cytochrome P450 (CYP) 7B1 is a steroid cytochrome P450 7α-hydroxylase that has been linked directly with bile salt synthesis and hereditary spastic paraplegia type 5 (SPG5). The enzyme provides the primary metabolic route for neurosteroids dehydroepiandrosterone (DHEA), cholesterol derivatives 25-hydroxycholesterol (25-HOChol), and other steroids such as 5α-androstane-3β,17β-diol (anediol), and 5α-androstene-3β,17β-diol (enediol). A series of investigations including homology modeling, molecular dynamics (MD), and automatic docking, combined with the results of previous experimental site-directed mutagenesis studies and access channels analysis, have identified the structural features relevant to the substrate selectivity of CYP7B1. The results clearly identify the dominant access channels and critical residues responsible for ligand binding. Both binding free energy analysis and total interaction energy analysis are consistent with the experimental conclusion that 25-HOChol is the best substrate. According to 20 ns MD simulations, the Phe cluster residues that lie above the active site, particularly Phe489, are proposed to merge the active site with the adjacent channel to the surface and accommodate substrate binding in a reasonable orientation. The investigation of CYP7B1-substrate binding modes provides detailed insights into the poorly understood structural features of human CYP7B1 at the atomic level, and will be valuable information for drug development and protein engineering.
    Chemistry 11/2012; · 5.93 Impact Factor
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    ABSTRACT: Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.
    The Journal of Physical Chemistry B 09/2012; 116(41):12415-25. · 3.61 Impact Factor
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    ABSTRACT: In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
    Journal of biomolecular structure & dynamics 06/2012; 30(6):716-27. · 4.99 Impact Factor
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    ABSTRACT: It is well known that electrides are a type of multielectron many-cage solid salt with excess electron anions inside the cages. The main concern regarding these structures is how to construct the organic single-caged electride molecules with an electron inside its cage. Using the perfluorinated fullerene cage C20F20 as the electron hole, the alkali metal atoms (M = Na, K) and superalkali atoms (M3O, M = Na, K) with a smaller vertical detachment energy (VDE) value as the source of the electrons, we can construct new nonlinear optical (NLO) organic single-caged electride salt molecules M+(e@C20F20)− and (M3O)+(e@C20F20)− due to the long-range charge transfer from the (super)alkali to inside the cage, forming an electron-hole pair within the molecule. To measure the nonlinear optical response, static first hyperpolarizabilities (β0) and the superalkali effect on β0 are exhibited for these new molecules. The β0 values are 400 and 600 au for M+(e@C20F20)− which are considerably smaller than 13000 and 10000 au for (M3O)+(e@C20F20)−. It is revealed that the superalkali effect on the β0 value is dramatic and the β0 value increases by about 20–30 times. New single-caged superalkali electride salt molecules (M3O)+(e@C20F20)− possess not only a large nonlinear optical property but also higher stability. They hold potential as high-performance nonlinear optical materials.
    Journal of Materials Chemistry 04/2012; 22(19):9652-9657. · 5.97 Impact Factor
  • Li-Tao Fan, Ying Li, Di Wu, Zhi-Ru Li, Chia-Chung Sun
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    ABSTRACT: A series of M2+(H5Aza222)–M′– (M = Be, Mg, Ca; M′ = Li, Na, K) alkalides that contain alkaline earth metal cations complexed by the H5Aza222– cage have been investigated using the CAM-B3LYP method. These alkaline earth-based alkalides not only present unusual structural features but also exhibit extraordinarily large static first hyperpolarizabilities (β0) up to 1.98 × 105 au. By comparing the β0 values among alkalides with various complexants, the Aza222 cage is found to be preferable to the previously investigated calix[4]pyrrole and n6adamanzane (n = 2, 3) complexants in enhancing the first hyperpolarizabilities of alkalides. In addition, the relationships between the β0 values of M2+(H5Aza222)–M′– and the atomic number of the M′– anion, the atomic number of the M2+ cation, and the M–M′ distance are explored.
    Australian Journal of Chemistry 03/2012; 65(2):138-144. · 1.87 Impact Factor
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    ABSTRACT: Alkane C-H bond activation by various catalysts and enzymes has attracted considerable attention recently, but many issues are still unanswered. The conversion of ethane to ethanol and ethene by bare [Fe(III)═O](+) has been explored using density functional theory and coupled-cluster method comprehensively. Two possible reaction mechanisms are available for the entire reaction, the direct H-abstraction mechanism and the concerted mechanism. First, in the direct H-abstraction mechanism, a direct H-abstraction is encountered in the initial step, going through a collinear transition state C···H···O-Fe and then leading to the generation of an intermediate Fe-OH bound to the alkyl radical weakly. The final product of the direct H-abstraction mechanism is ethanol, which is produced by the hydroxyl group back transfer to the carbon radical. Second, in the concerted reaction mechanism, the H-abstraction process is characterized via overcoming four/five-centered transition states (6/4)TSH_c5 or (4)TSH_c4. The second step of the concerted mechanism can lead to either product ethanol or ethene. Moreover, the major product ethene can be obtained through two different pathways, the one-step pathway and the stepwise pathway. It is the first report that the former pathway starting from (6/4)IM_c to the product can be better described as a proton-coupled electron transfer (PCET). It plays an important role in the product ethene generation according to the CCSD(T) results. The spin-orbital coupling (SOC) calculations demonstrate that the title reaction should proceed via a two-state reactivity (TSR) pattern and that the spin-forbidden transition could slightly lower the rate-determining energy barrier height. This thorough theoretical study, especially the explicit electronic structure analysis, may provide important clues for understanding and studying the C-H bond activation promoted by iron-based artificial catalysts.
    The Journal of Physical Chemistry A 02/2012; 116(5):1475-85. · 2.77 Impact Factor
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    ABSTRACT: The hydrogen abstraction of CH3OH by C2 (AΠu) has been investigated by direct ab initio dynamics over a wide temperature range 200–3000 K. The potential energy surfaces (PESs) have been constructed at the UCCSD(T)/aug-cc-pVTZ//UMP2/6-311++G(d,p) levels of theory. Two different hydrogen abstractions on the methyl and hydroxyl sites of methanol are considered. For the methyl H-abstraction, it is essentially a hydrogen atom transfer (HAT), whereas the hydroxyl site H-abstraction is better described as a proton coupled electron transfer (PCET) according to the Natural Bond Orbital (NBO) analysis. The results suggest that the methyl site reaction is dominant, and the calculated rate constants are roughly consistent with available experimental values. On the other hand, the temperature dependence of deuterium kinetic isotope effects (KIEs) analysis reveals a substantial normal isotope effect in the methyl H-abstraction process, while normal and inverse KIEs coexist in the hydroxyl H-abstraction channel. Furthermore, the three and four–parameter expressions of Arrhenius rate constants are also provided within 200–3000 K.
    Molecular Physics 01/2012; · 1.67 Impact Factor
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    Li-Tao FAN, Ying LI, Di WU, Zhi-Ru LI, Chia-Chung SUN
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    ABSTRACT: Using density functional theory with the B3LYP functional, the optimized structures of the organic alkalides M+ aza222M′- (M, M′ =Li, Na, K, and aza222=Azacryptand[2.2.2]) were calculated. The nonlinear optical (NLO) properties of these species were calculated by the BHandHLYP method. The results indicate that the M+aza222M′- alkalides exhibit very large first hyperpolarizabilities (β0) up to 1.0×106 a.u. (for M=Li, M′ =K). Both the first hyperpolarizabilities and the M-M′ distances of M+aza222M′- were found to depend on the atomic number of the alkali metal atom M(M′). By comparing the β0 values of various organic alkalides, aza222 was found to be preferable to the previously investigated complexants in enhancing the first hyperpolarizabilities of alkalides.
    ACTA PHYSICO-CHIMICA SINICA 01/2012; 28(3). · 0.87 Impact Factor
  • Jin-hui Zhan, Xi Zhao, Xu-ri Huang, Chia-chung Sun
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    ABSTRACT: The extracellular signal-regulated protein kinase 2 (ERK2) is a pivotal member involving in Ras/Raf/MEK/ERK signal transduction pathway, acting as a central point where multiple signaling pathways coalesce to drive transcription. The pyrazolylpyrrole compounds as ATP competitive inhibitors of ERK2 can bind target with a special binding mode and have higher inhibitory potency than other ERK2-inhibitors. We investigated the interaction mode of ERK2-inhibitor using molecular dynamics simulation. The molecular mechanics Poisson–Boltzmann surface area approach is used to calculate the binding free energy of ERK2 with pyrazolylpyrrole inhibitors to analyze the factors of improving the affinity. The results indicated that the electrostatic interactions play the most important role in keeping the stabilization of ERK2-inhibitor. The structural analyses showed that the protein motions can be controlled by changing the structures of inhibitors; furthermore, the full use of available space in the binding site by improving the flexibilities of inhibitors and introducing hydrophobic groups can increase the inhibitory effect.
    Journal of Theoretical and Computational Chemistry 11/2011; 08(05). · 0.52 Impact Factor
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    ABSTRACT: By means of the Homology modeling and the known structure of cyannogenic β-glycosidase from white clover (1CBG, EC 3.2.1.21), we construct a 3D model of the β-primeverosidase (EC 3.2.1.149) and search for the binding site of substrate. The 3D model is then refined by using molecular mechanics (optimization and molecular dynamics) simulation. Finally, the refined model is further assessed by Profile-3D and PROCHECK, and the results showed that the final model is reliable. Furthermore, the docking of the substrates into the active site of the protein indicates that β-primeverosidase is able to hydrolyze β-primeverosides, but not act on 2-phenylethyl β-D-glucopyranoside. These results suggest that β-primeverosidase shows broad substrate specificity with respect to the disaccharide glycon moiety (subsite -2). This is consistent with the experimental observation. Thr271 and Thr415 play important roles in subsite -2 of β-primeverosidase. Our results may be helpful for further experimental investigations.
    Journal of Theoretical and Computational Chemistry 11/2011; 05(spec01). · 0.52 Impact Factor
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    ABSTRACT: The reaction of N (4S) radical with NCO (X2Π) radical has been studied theoretically using density functional theory and ab initio quantum chemistry method. The triplet electronic state [N2CO] potential energy surface (PES) is calculated at the G3B3 and CCSD(T)/aug-cc-pVDZ//B3LYP/6-311++G(d,p) levels of theory. All the energies of the transition states and isomers in the pathway RP1 are lower than that of the reactants; the rate of this pathway should be very fast. Thus, the novel reaction N + NCO can proceed effectively even at low temperatures and it is expected to play a role in both combustion and interstellar processes. On the basis of the analysis of the kinetics of all pathways through which the reactions proceed, we expect that the competitive power of reaction pathways may vary with experimental conditions for the title reaction.
    Journal of Theoretical and Computational Chemistry 11/2011; 08(04). · 0.52 Impact Factor
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    ABSTRACT: We propose a multiscale simulation strategy to study the interplay between diffusion and curing reaction on the network formation and the corresponding mechanical properties of epoxy resins. Atomistic molecular dynamics simulations are first used to estimate the parameters that will be used in coarse-grained simulations. Then a dissipative particle dynamics coupled with curing reaction model is developed and adopted to simulate the cross-linking process of the system to form an epoxy network structure. We find that, during the curing process, to which extent that the components can diffuse between each other greatly influences the generated network structure. Finally, the reverse mapping of the coarse-grained structure to atomistic representation is carried out to analyze the mechanical properties and the Tg of the epoxy resin system.
    Macromolecules. 10/2011; 44(21).
  • Yan-Chun Li, Hong Liu, Xu-Ri Huang, Chia-Chung Sun
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    ABSTRACT: We apply the multibody dissipative particle dynamics method to exhibit evaporation- and surface-induced morphology of diblock copolymer thin films. We find that when the interactions between A components and B components of the diblock copolymer are symmetric, it is easy to obtain a lamellar morphology perpendicular to the surface. On the contrary, if the interactions between A-blocks and B-blocks are asymmetric, it is easy to obtain a lamellar morphology parallel to the surface. Spherical morphology and disorder morphology are formed when the solvent vapour and surface effect are considered. The order parameter and the film thickness are calculated during the phase-separation process for characterising the film properties. The attractive solvent vapour increases the film thickness and impacts the film morphology of the interface. The attractive surface decreases the film thickness and impacts the film morphology near the surface. Our results are partially helpful for the control of film morphology and film thickness in such kind of materials.
    Molecular Simulation 09/2011; 37(10):875-883. · 1.06 Impact Factor

Publication Stats

1k Citations
944.28 Total Impact Points

Institutions

  • 1988–2013
    • Jilin University
      • • State Key Lab of Theoretical and Computational Chemistry
      • • College of Chemistry
      • • Institute of Theoretical Chemistry
      • • Department of Chemistry
      Jilin, Jilin Sheng, China
  • 2002–2007
    • Heilongjiang University
      • School of Chemistry and Materials Science
      Jilin, Jilin Sheng, China
  • 2006
    • Harbin University of Science and Technology
      Charbin, Heilongjiang Sheng, China
  • 2003
    • California State University, Fullerton
      Fullerton, California, United States