Biomedical subjects

Chia-Chung Sun

Publications and source records attributed to Chia-Chung Sun.

At least 73 records · Page 4Linked to original sources

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 investigation of the large nonlinear optical properties of (HCN)n clusters with Li atom.

Two new classes of (HCN)(n)...Li and Li...(HCN)(n) (n = 1, 2, 3) clusters with the electride characteristic are formed in theory by the metal Li atom attaching to the (HCN)(n) (n = 1, 2, 3) clusters. Because of the interaction between the Li atom and the (HCN)(n) part, the 2s valence electron of the Li atom becomes a loosely bound excess electron. Our high-level ab initio calculations show that these new clusters with the excess electron have large first hyperpolarizabilities, for example, beta(0) = -15,258 au for (HCN)...Li and beta(0) = -3401 au for Li...(HCN) at the QCISD/6-311++G(3df,3pd) level (only beta(0) = -2.8 au for HCN monomer(26)). Obviously, the excess electron from the Li atom plays a crucial role in the large first hyperpolarizabilities of these clusters. The beta(0) value of (HCN)(n)...Li (beta(0) > 10(4) au, from sigma --> pi* transition) is larger than that of Li...(HCN)(n) (beta(0) > 10(3) au, from sigma --> sigma* transition) for n = 1, 2, or 3. In addition, two interesting rules have been observed. They are that |beta(0)| decreases with lengthening of the HCN chain for (HCN)(n)...Li clusters and that |beta(0)| increases as n increases for Li...(HCN)(n) clusters. In this paper, we discuss two classes of clusters that are highly similar to the electride structure model, of which the structural characteristics are that alkali metal atoms ionize to form cations and trapped electrons under the action of other polar molecules. Thus, the investigation on the large first hyperpolarizabilities of (HCN)(n)...Li and Li...(HCN)(n) (n = 1, 2, 3) may prompt one to study the unusual nonlinear optical responses of some electrides.

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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

The static polarizability and first hyperpolarizability of the water trimer anion: ab initio study.

This work predicts the extraordinary hyperpolarizability of inorganic clusters: two water trimer anions. The first hyperpolarizabilities of (H2O-)(3) are considerable, beta(0)=1.715 x 10(7) a.u. for configuration A and beta(0)=1.129 x 10(7) a.u. for configuration B at MP2/d-aug-cc-pVDZ+x level. The first hyperpolarizabilities of (H2O-)(3) (configuration A) and related systems [(H2O)(3) and (H2O)(3)F-] are compared at the MP2/d-aug-cc-pVDZ+x level. These results are beta(0)=1.715 x 10(7) a.u. for (H2O-)(3), beta(0)=35 a.u. for (H2O)(3) [the neutral core of (H2O-)(3)], and beta(0)=46 a.u. for (H2O)(3)F-). Comparing the beta(0) values of related systems, we find that the dipole-bound excess electron is the key factor in the extraordinary first hyperpolarizability of (H2O-)(3) species. It will provide a future in the development of some materials with the excess electron (e.g., electrides) that exhibit large nonlinear optical response.

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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

Characteristic of structures and pi-hydrogen bond of dimers C2H4-nFn-HF (n=0,1,2).

By the counterpoise-correlated potential energy surface method (interaction energy optimization), five structures of the C(2)H(4-n)F(n)-HF (n = 0,1,2) dimers with all real frequencies have been obtained at MP2/aug-cc-pVDZ level. The influence of F substituent effect on the structure and pi-hydrogen bond of dimer has been discussed. For C(2)H(4-n)F(n)-HF (n = 1,2), the pi-hydrogen bonds are elongated comparing with that for C(2)H(4)-HF. For C(2)H(3)F-HF, g-C(2)H(2)F(2)-HF, cis-C(2)H(2)F(2)-HF, the pi-hydrogen bonds are further deformed. These changes (elongate, shift, and deformation) of pi-hydrogen bond mainly come from deformation of pi-electron cloud of C=C bond. The pi-electron cloud is pushed towards the one C atom, the pi H-bond shift also to the C direction. Since the two lobes of pi-electron cloud have deviated slightly from the molecular vertical plane passing through C=C bond, the pi-hydrogen bond is sloped. Intermolecular interaction energies of the dimers are calculated to be -3.9 for C(2)H(4)-HF, -2.8 for C(2)H(3)F-HF, -2.1 for g-C(2)H(2)F(2)-HF, -1.6 for cis-C(2)H(2)F(2)-HF, -1.3 kcal/mol for trans-C(2)H(2)F(2)-HF, at CCSD(T)/aug-cc-pVDZ level.

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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

Si2CN: a stable nitrogen-containing radical with cyclic ground state.

The structures and isomerization of Si(2)CN species are explored at density functional theory and ab initio levels. Fourteen minimum isomers are located connected by 23 interconversion transition states. At the coupled-cluster single double (CCSD)(T)/6-311+G(2df)//QCISD/6-311G(d) +zero-point vibrational energies level, the thermodynamically most stable isomer is a four-membered ring form cSiSiCN 1 with Si-C cross bonding. Isomer 1 has very strong C-N multiple bonding characters, formally suggestive of a radical adduct between Si(2) and CN. Such a highly pi-electron localization can effectively stabilize isomer 1 to be the ground state. The second low-lying isomer is a linear form SiCNSi 5 (9.8 kcal/mol above 1) with resonating structure among [Si=C-*N=Si], *[Si=C=N=Si], and [Si=C=N-Si*]* with the former two bearing more weight. The species 1 and 5 have very high kinetic stability stabilized by the barriers of at least 25 kcal/mol. Both isomers should be experimentally or astrophysically observable. In light of the fact that no cyclic nitrogen-containing species have been detected in space, the cyclic species 1 could be a very promising candidate. The calculated results are compared to those of the analogous molecules C(3)N, C(3)P, SiC(2)N, and SiC(2)P. Implications of Si(2)CN in interstellar and N-doped SiC vaporization processes are also discussed.

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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

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

An ab initio theoretical prediction: an antiaromatic ring pi-dihydrogen bond accompanied by two secondary interactions in a "wheel with a pair of pedals" shaped complex FH . . . C4H4 . . . HF.

By the counterpoise-correlated potential energy surface method (interaction energy optimization), the structure of the pi H-bond complex FH cdots, three dots, centered FH . . . C4H4 . . . HF has been obtained at the second-order Møller-Plesset perturbation theory (MP2/aug-cc-pVDZ) level. Intermolecular interaction energy of the complex is calculated to be -7.8 kcal/mol at the coupled-cluster theory with single, double substitutions and perturbatively linked triple excitations CCSD (T)/aug-cc-pVDZ level. The optimized structure is a "wheel with a pair of pedals" shaped (1mid R:1) structure in which both HF molecules almost lie on either vertical line passing through the middle-point of the C[Double Bond]C bond on either side of the horizontal plane of the C4 ring for cyclobutadiene. In the structure, an antiaromatic ring pi-dihydrogen bond is found, in which the proton acceptor is antiaromatic 4 electron and 4 center pi bond and the donors are both acidic H atoms of HF molecules. In accompanying with the pi-dihydrogen bond, two secondary interactions are exposed. The first is a repulsive interaction between an H atom of HF and a near pair of H atoms of C4H4 ring. The second is the double pi-type H bond between two lone pairs on a F atom and a far pair of H atoms.

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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↗