Biomedical subjects

Chia-Chung Sun

Publications and source records attributed to Chia-Chung Sun.

At least 55 records · Page 3Linked to original sources

PubMed2005

The trigonal bipyramidal MN3M species: a new kind of aromatic complex containing a multiple-fold aromatic N3 subunit.

A new kind of aromatic trigonal bipyramidal MN3M (M=Be, B, Mg, Al, and Ca) species, with all real frequencies, is obtained at the MP2/6-311+G(3d) level. The nucleus-independent chemical shift values are -102.16 ppm for the N3 (3-) ring, and -74.09, -79.39, -65.06, -74.44, and -62.33 ppm (at the geometrical center of the trigonal bipyramid) for BeN3Be, BN3B, MgN3Mg, AlN3Al, and CaN3Ca, respectively. Molecular orbital analysis indicates that the regular triangular N3 (3-) ring and each MN3M species have three aromatic six-electron systems (pi, sigma(p), and sigma(s)) and exhibit threefold aromaticity. The CaN3Ca species has a very low vertical ionization energy of 3.64 eV at the CCSD(T)/6-311+G(3d) level, which is even lower than the ionization energy (3.9 eV) of the Cs atom. Therefore, CaN3Ca can be considered as a new superalkali species. A further study on the CaN3CaCl molecule confirms the superalkali characteristics of CaN3Ca. Two interesting phenomena are explored in the MN3M species: the delocalized electron cloud of the N3 subunit is elongated by two M cations, and the electron clouds of two M cations are distended by the N3 (3-) ring.

Journal Article↗

PubMed2005

Li3-O-Li3 molecule: a metal-nonmetal-metal sandwichlike compound with a distending electron cloud.

The D3d and D2d isomers of the Li3-O-Li3 molecule are metal-nonmetal-metal sandwichlike structures that contain two Li3 superalkali atoms. Their geometries and the real frequencies are obtained at the CCSD(T)/aug-cc-pVDZ level. They are different from the traditional types of the nonmetal-metal-nonmetal sandwich compounds. The natural bond orbital calculation and the topological property nabla2rho(r) calculation indicate that they are typical ionic compounds. In two isomers, the O2- anion is sandwiched in between two Li3+ cation rings. However, the different orientations of two Li3+ planes give the D3d isomer its own special characteristics. Under the action of the O2- anion in the center, the valence electrons of the D3d isomer are pushed out from two Li3+ triangle rings. This special interaction causes three phenomena. First, the valence electron clouds are distended. Second, the vertical ionization energy of the D3d isomer is considerably low, 4.39 eV, so that it may also be viewed as a superalkali atom. Third, we find that the D3d isomer owns the out-of-plane aromaticity and the largest negative nucleus-independent chemical shift value (-10.8 ppm) exists at 2.5 A above the center of the Li3+ ring, not at the center of the Li3+ ring like the isolated aromatic Li3+ cation.

Journal Article↗

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

Asymmetrical linear structures including three-electron hemibonds or other interactions in the (ABA)-type triatomic cations: Ne3+, (He-Ne-He)+, (Ar-Ne-Ar)+, (Ar-O-Ar)+, (He-O-He)+, and (Ar-He-Ar)+.

By the counterpoise geometry optimization at the level of CCSD(T)aug-cc-pVDZ, the asymmetrical linear structures with all the real frequencies were obtained for the triatomic cations of (ABA)+ type: Ne3+, (He-Ne-He)+, (Ar-Ne-Ar)+, (Ar-He-Ar)+, (He-O-He)+, and (Ar-O-Ar)+. The validity of this optimization method is confirmed by comparing with the method of the potential-energy surface for the calculations of Ne3+ and (He-Ne-He)+. Using the molecular-orbital theory, it is found that the interaction within the triatomic cations is dominated by the contribution from the first two atoms while the contribution from the third atom is small. This result is justified as a direct consequence of forming an asymmetrical linear structure. Specifically, four types of interaction within the triatomic cations are identified: three-electron sigma-type hemibond, three-electron pi-type hemibond, two-electron sigma bond, and the attraction between cation and atoms. For Ne3+, (He-Ne-He)+, and (He-O-He)+ clusters, it is shown that the electron correlation effect supports the asymmetry.

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

Mechanism of HCS + O2 reaction: hydrogen- or oxygen-transfer?

In spite of the potential importance of the HCS radical in both combustion and interstellar processes, its chemical reactivity has not been tackled previously. In the present paper, the oxidation reaction of the HCS radical is theoretically investigated for the first time at the CCSD(T)/6-311++G(3df,2p)//BH&HLYP/6-311++G(d,p)+ZPVE and Gaussian-3//B3LYP/6-31G(d) levels. It is shown that the most feasible pathway is the O2 addition to the HCS radical forming the intermediate SC(H)OO which can undergo a subsequent O-extrusion leading to SC(H)O + 3O. This features an indirect O-transfer mechanism with the overall barrier of 4.4 and 3.5 kcal mol(-1), respectively, at the two levels. However, formation of the H-transfer product CS + HO2 is kinetically much less feasible, i.e., the direct mechanism has barriers of 14.3 and 8.7 kcal mol(-1), whereas the indirect mechanism has barriers of 12.6 and 10.7 kcal mol(-1), respectively. This result is in sharp contrast to the analogous HCO + O2 reaction, where the direct (with a barrier of 2.98 kcal mol(-1)) and indirect (2.26 kcal mol(-1)) H-transfer processes are highly competitive over the indirect O-transfer process (the least endothermicity is 19.9 kcal mol(-1)). The possible explanations and implications of the present results are provided.

Algorithms↗

PubMed2005

The structure and the large nonlinear optical properties of Li@calix[4]pyrrole.

A new compound with electride characteristics, Li@calix[4]pyrrole, is designed in theory. The Li atom in Li@calix[4]pyrrole is ionized to form a cation and an excess electron anion. Its structure with C(4v) symmetry resembles a cup-like shape. It may be a stable organic electride at room temperature. The first hyperpolarizability of the cup-like electride molecule is first investigated by the DFT (B3LYP) method. The result shows that this electride molecule has a considerably large first hyperpolarizability with beta(0) = 7326 au (63.3 x 10(-30) esu), while the beta(0) value of the related calix[4]pyrrole system is only 390 au. Obviously, the Li atom doped in calix[4]pyrrole brings a dramatic change to the electronic structure, so that the first hyperpolarizability of Li@calix[4]pyrrole is almost 20 times larger than that of calix[4]pyrrole. We find that the excess electron from the Li atom plays an important role in the large first hyperpolarizability of Li@calix[4]pyrrole. The present investigation reveals a new idea and different means for designing and synthesizing high-performance NLO materials.

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

Inverse sodium hydride: density functional theory study of the large nonlinear optical properties.

"Inverse sodium hydride" (AdzH(+)Na-) is an alkalide compound synthesized in recent experiments containing the unusual charge distribution H+ and Na- (inverse charge state). The new class of compounds interests scientists to investigate their especial structures and properties. In this paper, the structures of three alkalides compounds, (Me)3NH(+)Na-, AdzH(+)Na-, and AdzLi(+)Na-, have been obtained in theory. Especially, the structure of AdzLi(+)Na- is still researched by experimental scientists. We investigated the NLO properties of the alkalides complexes for the first time and found that inverse sodium hydride AdzH(+)Na- has a considerably large NLO response beta0 = 5.7675 x 10(4) au by density functional theory (DFT). To understand the essential features of the large NLO properties, four related systems have been also calculated. Their first hyperpolarizabilities are beta0 = 7.357 x 10(3) au for (Me)3NH(+)Na-, beta0 = 3.9 au for (Me)3NH+, beta0 = 1.10 x 10(2) au for (Me)3NH(+)Cl-, and beta0 = 6.20681 x 10(5) au for AdzLi(+)Na-, respectively. By comparing, we found that, first, the Na- anion plays a crucial role in the considerably large first hyperpolarizability of inverse sodium hydride and, second, the first hyperpolarizability of inverse sodium hydride increases with the charge value of the sodium anion. The above results are useful for designing potential NLO materials.

Journal Article↗

PubMed2005

Study of pi halogen bonds in complexes C2H(4-n)Fn-ClF (n = 0-2).

The pi-halogen bond may be considered, in a broad sense, essentially a pi-hydrogen bond. Using the counterpoise-corrected potential energy surface method (interaction energy optimization), the stationary structures of the C2H(4-n)Fn-ClF (n = 0-2) complexes with all real frequencies have been obtained at the MP2/aug-cc-pVDZ level. For C2H(4-n)Fn-ClF (n = 0-2), the pi-halogen bond has a long distance and is elongated by the F substituent effect. The pi-halogen bond length order is 2.661 A for C2H4-ClF < 2.745 A for C2H3F-ClF < 2.766 A for g-C2H2F2-ClF < 2.8076 A for trans-C2H2F2-ClF < 2.8079 A for cis-C2H2F2-ClF. For three complexes C2H3F-ClF, g-C2H2F2-ClF, and cis-C2H2F2-ClF, the pi-halogen bonds are further shifted and sloped by the F substituent effect. The F substituent effect reduces also the interaction energy of the pi-halogen bond. The interaction energies are respectively -3.7 for C2H4-ClF, -2.8 for C2H3F-ClF, -2.3 for g-C2H2F2-ClF, -1.9 for cis-C2H2F2-ClF, and -1.8 kcal/mol for trans-C2H2F2-ClF, at the CCSD(T)/aug-cc-pVDZ level. The electron correlation contribution of the interaction energy is large for C2H(4-n)Fn-ClF (n = 0-2), which shows that the stabilities of the pi-halogen bond systems results primarily from the dispersion interaction. In the double F substituent systems, the interaction energy of the pi-halogen bond structure with a longer interaction distance is larger than that of the corresponding pi-hydrogen bond structure with a shorter interaction distance. This may be because there are the large electron correlation contributions of the interaction energy, and a secondary interaction between lone pairs of Cl atom and some atoms (H, C) with positive charges in the pi-halogen bond structure.

Chlorides↗

PubMed2005

Theoretical study on stability and properties of NC2O isomers.

The structures, energetics, spectroscopies, and stabilities of the doublet NC(2)O radical are explored at density functional theory and ab initio levels. Nine minimum isomers are located connected by 22 interconversion transition states. At the CCSD(T)/6-311+G(2df)//QCISD/6-311G(d)+ZPVE level, the lowest-lying isomer is bent NCCO 1 (0.0 kcal/mol) with (2)A' state followed by bent isomer CNCO 2 (16.7). Two isomers (1 and 2) and another high-lying species CCNO 4 (99.4) with bent structure are considerably stabilized by a barrier of at least 20 kcal/mol. All of the three isomers should be experimentally or astrophysically observable. This result is consistent with their indication of neutralization-reionization mass spectrometry experiments. Also, the calculated spectroscopic properties and bond distances of known NCCO 1 are consistent with recent experimental observations and theoretical studies. The bonding natures of the isomers 1, 2, and 4 are analyzed. Their molecular properties including the heats of formation, adiabatic ionization potentials, and adiabatic electronic affinities are calculated at the higher levels G3//B3LYP, G3(MP2)//B3LYP, QCISD, and CCSD(T) (single-point). Possible formation strategies of the isomers 1, 2, and 4 in laboratory and space are also discussed in detail.

Journal Article↗

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↗

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.

Journal Article↗

PubMed2005

Theoretical study on structures and stability of C4P isomers.

The structures, energetics, spectroscopies, and stabilities of doublet C(4)P isomeric species are explored at the DFT/B3LYP, QCISD, and CCSD(T) (singlet-point) levels. A total of 12 minimum isomers and 27 interconversion transition states are located. At the CCSD(T)/6-311G(2df)//QCISD/6-311G(d)+ZPVE level, the lowest-lying isomer is a floppy CCCCP 1 (0.0 kcal/mol) mainly featuring a cumulenic structure |C=C=C=C=P*|, which differs much from the analogous C4N radical (|*C-C[triple bond]C-C[triple bond]N|). The quasi-linearity and the low bending mode of 1 are in contrast to the previous prediction. The second energetically followed isomer PC-cCCC 3 (14.9 kcal/mol) possesses a CCC ring-bonded to CP. The two low-lying isomers are separated by a high-energy ring-closure/open transition state (26.5 kcal/mol) and thus are very promising candidates for future laboratory and astrophysical detection. Furthermore, four high-energy isomers, that is, two bent isomers CCPCC 2 (68.4 kcal/mol) and CCPCC 2' (68.5 kcal/mol) and two cagelike species 10 (56.0 kcal/mol) and 11 (67.9 kcal/mol), are also stabilized by considerable barriers. The present work is the first detailed potential energy survey of CnP clusters and can provide useful information for the investigation of larger CnP radicals and for understanding the isomerism of P-doped C vaporization processes.

Journal Article↗

PubMed2005

Radical-molecule reaction C3H+H2O: a mechanistic study.

Despite the importance of the C(3)H radical in both combustion and interstellar space, the reactions of C(3)H toward stable molecules have never been studied. In this paper, we report our detailed mechanistic study on the radical-molecule reaction C(3)H+H(2)O at the Becke's three parameter Lee-Yang-Parr-B3LYP6-311G(d,p) and coupled cluster with single, double, and triple excitations-CCSD(T)6-311G(2d,p) (single-point) levels. It is shown that the C(3)H+H(2)O reaction initially favors formation of the carbene-insertion intermediates HCCCHOH (1a,1b) rather than the direct H- or OH-abstraction process. Subsequently, the isomers (1a,1b) can undergo a direct H- extrusion to form the well-known product propynal HCCCHO (P(5)). Highly competitively, (1a,1b) can take the successive 1,4- and 1,2-H-shift interconversion to isomer H(2)CCCHO(2a,2b) and then to isomer H(2)CCHCO(3a,3b), which can finally take a direct C-C bond cleavage to give product C(2)H(3) and CO (P(1)). The other products are kinetically much less feasible. With the overall entrance barrier 10.6 kcal/mol, the title reaction can be important in postburning processes. Particularly, our calculations suggest that the title reaction may play a role in the formation of the intriguing interstellar molecule, propynal HCCCHO. The calculated results will also be useful for the analogous C(3)H reactions such as with ammonia and alkanes.

Journal Article↗

PubMed2005

Proton transfer of NH3-HCl catalyzed by only one molecule.

The proton transfer in NH(3)-HCl by only one molecule of catalyst was studied by using the MP2 method with the large 6-311++G(2d,2p) basis set. The 18 structures are obtained for the smallest units, NH(3)-HCl-A trimers, for which the proton transfer maybe occurred. The final results show that the proton transfers have occurred in the 15 cyclic shape structures for A = H(2)SO(4), H(2)SO(3), HCOOH (a), HF, H(2)O(2), HNO(3), HNO(2) (a), CH(3)OH, HCl, HNC, H(2)O, HNO(2) (b), NH(3), HCOOH (b), and HCHO, and not occurred in another 3 trimer structures for A = HCN, H(2)S, and PH(3). These results show that the proton transfer occurs from HCl to NH(3) when catalyst molecule A (acidic, neutral, or basic) not only as a proton donor strongly donates the proton to the Cl atom but as an acceptor strongly accepts the proton from the NH(3) molecule in the cyclic H-bond structure. In this work, a proton circumfluence model is proposed to explain the mechanism of the proton transfer. We find that, for the trimer, when the sum of two hydrogen bond lengths (R = R(1) + R(2)) is shorter than 5.0 A, molecule A has the ability to catalyze the proton transfer. In addition, we also find that the interaction energy E(int) between NH(3)-HCl and A is nearly related to the extent (R(H1)(-)(Cl)) of proton transfer, that is, the interaction energy E(int) increases with the proton transfer.

Ammonia↗