Biomedical subjects

Chia-Chung Sun

Publications and source records attributed to Chia-Chung Sun.

At least 19 recordsLinked to original sources

PubMed2007

A theoretical investigation of the excited states of OCLO radical, cation, and anion using the CASSCF/CASPT2 method.

Using the complete active space self-consistent field method with a large atomic natural orbital basis set, 10, 13, and 9 electronic states of the OClO radical, OClO(+) cation, and OClO(-) anion were calculated, respectively. Taking the further correlation effects into account, the second-order perturbation (CASPT2) calculations were carried out for the energetic calibration. The photoelectron spectroscopy of the OClO radical and OClO(-) anion were extensively studied in the both case of the adiabatic and vertical ionization energies. The calculated results presented the relatively complete assignment of the photoelectron bands of the experiments for OClO and its anion. Furthermore, the Rydberg states of the OClO radical were investigated by using multiconfigurational CASPT2 (MS-CASPT2) theory under the basis set of large atomic natural orbital functions augmented with an adapted 1s1p1d Rydberg functions that have specially been built for this study. Sixteen Rydberg states were obtained and the results were consistent with the experimental results.

Journal Article↗

PubMed2007

Design of sandwichlike complexes based on the planar tetracoordinate carbon unit CAl4(2-).

Ever being a large curiosity, a series of simple "planar tetracoordinate carbon (ptC)" molecules have been recently characterized by experiments. Incorporation of such exotic ptC units into the assembled molecular materials, which will bridge the isolated clusters in molecular beams and the potential solid materials, is very challenging. In this paper, we described the first attempt on how to assemble the fewest-number ptC unit CAl42- into molecular materials in sandwich forms on the basis of the density functional theory calculations on a series of model compounds [D(CAl4)M]q- as well as the saturated compounds [D(CAl4)Mn] ((D = CAl42-, Cp-(C5H5-); M = Li, Na, K, Be, Mg, Ca). For M = Li, Be, Mg, and Ca, the ptC unit CAl42- can only be assembled in our newly proposed "heterodecked sandwich" scheme (e.g., [Cp(CAl4)M]q- (M = Li, Na, K, q = 2; M = Be, Mg, Ca, q = 1)) so as to avoid cluster fusion. For M = Na and K, the ptC unit CAl42- can be assembled in both the traditional "homodecked sandwich" [(CAl4)2M]q- (M = Li, Na, K, q = 3; M = Be, Mg, Ca, q = 2) and the novel heterodecked sandwich schemes. Moreover, the counterions were found to have an important role in determining the type of the ground structures for the homodecked sandwich. Various assembled species in extended frameworks were designed. Notably, among all the designed sandwich species, the ptC unit CAl42- generally prefers to interact with the partner deck at the side (Al-Al bond) or corner (Al atom) site. This has not been reported in the sandwich complexes on the basis of the known decks such as Cp-, P5-, N42-, and Al42-, for which only the traditional face-face interaction type was considered. Our results for the first time showed that the ptC unit CAl42- can act as a new type of "superatom". The present results are expected to enrich the flat carbon chemistry, superatom chemistry, metallocenes, and combinational chemistry.

Journal Article↗

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

Sandwich-like compounds based on the all-metal aromatic unit Al(4)2- and the main-group metals M (M=Li, Na, K, Be, Mg, Ca).

Inspired by the pioneering experimental characterisation of the all-metal aromatic unit Al(4)2- in the bimetallic molecules MAl4- (M=Li, Na, Cu) and by the very recent theoretical design of sandwich-type transition-metal complexes [Al4MAl4]q- (q=0-2; M=Ti, V, Cr, Zr, Nb, Mo, Hf, Ta, W), we used density functional theory (DFT) calculations (B3LYP/6-311+G(d) to design a series of novel non-transition-metal sandwich complexes based on the all-metal aromatic unit Al4(2-) and the main-group metals M (M=Li, Na, K, Be, Mg, Ca). The traditional homo-decked sandwich compounds [Al4MAl4]q- (without counterions) and (nM)q+[Al4MAl4]q- (with counterions M) (q=2-3, M=Li, Na, K, Be, Mg, Ca), although some of them are truly energy minima, have a much higher energy than many fused isomers. We thus concluded that it seems unlikely for Al4(2-) to sandwich the main-group metal atoms in the homo-decked sandwich form. Alternatively, we proposed a new type of sandwich complex, namely hetero-decked sandwich compounds [CpMAl4]q-, that are the ground-state structures for each M both with and without counterions. It was shown that with the rigid Cp- partner, the all-metal aromatic unit Al(4)2- might indeed act as a "superatom". These new types of all-metal aromatic unit-based sandwich complexes await future experimental verification.

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

Theoretical investigation of one-photon and two-photon absorption properties for multiply N-confused porphyrins.

We have theoretically investigated a series of multiply N-confused porphyrins and their Zn or Cu complexes for the first time by using DFT(B3LYP/6-31G*) and ZINDO/SOS methods. The electronic structure, one-photon absorption (OPA), and two-photon absorption (TPA) properties have been studied in detail. The calculated results indicate that the OPA spectra of multiply N-confused porphyrins are red-shifted and the OPA intensities decrease compared to normal porphyrin. The maximum two photon absorption wavelengths lambda(max) are blue-shifted and the TPA cross sections delta(max) are increased 22.7-112.1 GM when the N atoms one by one are inverted from core to beta position to form multiply N-confused porphyrins. Especially delta(max) of N3CP get to 164.7 GM. The electron donors -C6F5s at meso-position can make the TPA cross section delta(max) increase. After forming metal complexes with Cu or Zn, the TPA properties of multiply N-confused porphyrins are further increased except for N3CP, N4CP. Our theoretical findings demonstrate that the multiply N-confused prophyrins as well as their metal complexes and derivatives are promising molecules that can be assembled series of materials with large TPA cross section, and are sure to be the subject of further investigation.

Journal Article↗

PubMed2006

Ab initio studies on isomers of macropolyhedral borane ions [B20H18]n (n = 0, -2, -4).

Various isomers of macropolyhedral borane ions [B20H18]n (n = 0, -2, -4) are investigated by using the density functional theory methods at RB3LYP/6-31+G* and RB3LYP/6-31G* levels to obtain the optimized geometries, harmonic vibrational frequencies, electron structures, and the stability order. The calculated results show that optimized bond lengths are consistent with the available experimental values and the natural populations, taking [a2 -B20H18]4- (4) as an example, are also in agreement with NMR spectra. The calculated vibrational frequencies are all real, so all of these isomers could be stable, among which [a2 -B20H18]2- (3) and [a2 -B20H18]0 (7) are considered for the first time in this paper. On the basis of the contour maps of molecular orbitals, the delocalized characteristic of molecular orbitals and the possible redox mechanism of these ions are also discussed. Moreover, the analysis on counting of skeletal bonding electrons shows that the isomers (1)-(6) obey the electronic requirement predicted by the mno rule, whereas the newly predicted isomer (7) does not match the mno rule.

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

Theoretical mechanistic study on the radical-molecule reactions of cyanomethylidyne with PH3, H2S, and HCl.

The cyanomethylidyne (CCN) has been the long-standing subject of extensive theoretical and experimental studies on its structures and spectroscopies. However, there are few investigations on its reactivity. Our very recent theoretical work indicated that even with the simplest methane, the CCN reaction faces almost zero barriers following the carbyne mechanism as CH does. This was suggestive of the powerfulness of the nonatomic and nonhydrogenated CCN radical in depleting old molecules and synthesizing new cyanogen-containing molecules in either combustion or interstellar processes. In this paper, a detailed mechanistic study at the CCSD(T)/6-311+G(2df,p)//B3LYP/6-311g(d,p) and G2M(CC1)//B3LYP/6-311G(d,p) computational levels is reported for the reactions of CCN with a series of sigma-bonded molecules of the second row H(n)X (X,n) = (P,3), (S,2), and (Cl,1). The carbenoid insertion is confirmed as the most favored entrance channel, forming H(n) (-1)XC(H)CN. Subsequently, H(n) (-1)XC(H)CN will predominantly lead to product H(n) (-2)XC(H)CN+H via the H-extrusion processes (except X = Cl). Yet, the CCN+HX (X = Cl) reaction is the exception because XC(H)CN intrinsically has no H-atoms at X for extrusion or migration. At G2M(CC1)//B3LYP/6-311G(d,p) computational level, ClC(H)CN can only dissociate back to the reactant or be stabilized with its isomers upon sufficient collisions or radiation. The carbyne character confirmed in this paper provides a useful base for future experimental and theoretical study on the chemistry of this nonatomic and nonhydrogenated reactive radical. In addition, interestingly, the complexes H(n)X-CCN (X,n) = (P,3) and (S,2) formed in the reactions are found not to be the simple (loosely bound) donor-accepter complexes as those formed in the CCN insertions into other hydrides (NH(3), H(2)O, HF, HCl). On the basis of the comparison with the qualitative features of typical ylides, H(3)P--CCN and H(2)S--CCN are considered to be similar to the ylides in nature, being "ylide-like radicals." They might be observed in some experiments, since they are in deep potential wells on the energy surface.

Computer Simulation↗

PubMed2006

Theoretical study of two-photon absorption properties of a series of ferrocene-based chromophores.

The electronic structures, one-photon absorption (OPA), and two-photon absorption (TPA) properties of a series of ferrocene-based chromophores with TCF-type acceptors (TCF = 2-dicyanomethylene-3-cyano-4-methyl-2,5-dihydrofuran) have been studied by using the ZINDO-SOS method. The results have revealed that OPA and TPA of ferrocenyl derivatives are affected by the strength of the acceptor, especially the pi-bridge conjugation length. The TPA cross section increases with increasing acceptor strength and pi-bridge conjugation length. The TCF-type acceptor with a phenyl group can lead to a larger TPA cross section. Quadrupole molecules have the largest TPA cross sections (2000-3000 GM), which are about 4 times that of the corresponding dipolar molecules, indicating larger interactions between the top and bottom branches. Finally, the origins of the two-photon excitations for ferrocenyl derivatives are analyzed. The calculations show that ferrocenyl derivatives with TCF-type acceptors (especially quadrupole molecules) are promising candidates for TPA materials.

Journal Article↗

PubMed2006

Theoretical studies on the low-lying electronic states of the HSO neutral radical and its cation.

Using the complete active space self-consistent field (CASSCF) method with large atomic natural orbital (ANO-L) basis set, four electronic states of the HSO neutral radical are optimized. The vertical transitions of the HSO neutral radical are investigated by using the same method under the basis set of ANO-L functions augmented with a series of adapted 1s1p1d Rydberg functions, through which eight valence states and eight Rydberg states are probed. Ionic states of the HSO neutral radical are extensively studied in both cases of the adiabatic and vertical ionization, from which the relatively complete understanding of ionization energies is given. To include further correlation effects, the second-order perturbation method (CASPT2) is implemented, and the comparison between CASSCF and CASPT2 methods is performed.

Journal Article↗

PubMed2006

Ab initio study of the spectroscopy of CH3N and CH3CH2N.

Complete active space (CAS) calculations with 6-311++g(3df,3pd) basis sets were performed for a large number of electronic states of the nitrate free radical (CH3N/CH3CH2N) and their positive and negative ions. All calculated states are valence states, and their characters are discussed in detail. To investigate the Jahn-Teller effect on the CH3N radical, Cs symmetry was used for both CH3N and CH3CH2N in calculations. The results (CASPT2 adiabatic excitation energies and CASSI oscillator strengths) suggest that the calculated transitions of CH3N at 32172 and 32139 cm(-1) are attributed to the 2(3)A' ' --> 1(3)A' ' and 1(3)A' --> 1(3)A' ', respectively, which is in accordance with the A3E --> X3A2 emission spectrum at T0 = 31 817 cm(-1). The calculated transitions of CH3CH2N at 334 nm are attributed to the 1(3)A' ' --> 2(3)A' ' and 1(3)A' ' --> 1(3)A', respectively, which is in accordance with the UV absorption spectrum of a series of 11 bands beginning at 335 nm. The vertical and adiabatic ionization energies were obtained to compare with the PES data. These results are in agreement with previous experimental data, which is discussed in detail.

Electrons↗

PubMed2006

Do single-electron lithium bonds exist? Prediction and characterization of the H3C...Li-Y (Y=H, F, OH, CN, NC, and CCH) complexes.

A new kind of single-electron lithium bonding complexes H(3)C...LiY (Y=H, F, OH, CN, NC, and CCH) was predicted and characterized in the present paper. Their geometries (C(3v)) with all real harmonic vibrational frequencies were obtained at the MP2/aug-cc-pVTZ level. For each H(3)C...LiY complex, single-electron Li bond is formed between the unpaired electron of CH(3) radical and positively charged Li atom of LiY molecule. Due to the formation of the single-electron Li bond, the C-H bonds of the CH(3) radical bend opposite to the LiY molecule and the Li-Y bond elongates. Abnormally, the three H(3)C...LiY (Y=CN, NC, and CCH) complexes exhibit blueshifted Li-Y stretching frequencies along with the elongated Li-Y bonds. Natural bond orbital analyses suggest ca. 0.02 electron transfer from the methyl radical (CH(3)) to the LiY moiety. In the single occupied molecular orbitals of the H(3)C...LiY complexes, it is also seen that the electron could of the CH(3) radical approaches the Li atom. The single-electron Li bond energies are 5.20-6.94 kcal/mol for the H(3)C...LiY complexes at the CCSD(T)aug-cc-pVDZ+BF (bond functions) level with counterpoise procedure. By comparisons with some related systems, it is concluded that the single-electron Li bonds are stronger than single-electron H bonds, and weaker than conventional Li bonds and pi-Li bonds.

Biophysics↗

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

Theoretical study of photodissociation dynamics on the lowest-lying Rydberg state of ketene.

In the present study, an attempt is made to reveal the main mechanism of photodissociation on the lowest-lying Rydberg state (1)B(1) of ketene, referred to as the second singlet excited state S(2), by means of the complete active space self-consistent field and the second-order multiconfigurational perturbation theory methods. The located S(2)S(1)T(1) three-surface intersection plays an important role in the dissociation process. It is shown that the intersection permits an efficient internal conversion from S(2) to S(1) state, but prohibits the intersystem crossing from S(2) to T(1) state because of the small spin-orbital coupling value of 0.136 cm(-1). The main photodissociation process could be described as follows: after one photon absorption to the S(2) state, ketene preferentially relaxes to the minimum S(2)C(2v), and undergoes a transition state S(2)TS with small potential barrier along the C(s)-I (out-of-plane bent) symmetry, and passes through the S(2)S(1)T(1) intersection to reach S(1) surface, then arrives at the transition state S(1)TS along the minimum energy path. As is well known, S(1)-->S(0) internal conversion around the Franck-Condon region is expected to be very efficient, and eventually the hot S(0) molecule has accumulated enough energy to yield the CH(2) (a (1)A(1)) and CO (X (1)Sigma(+)) products.

Journal Article↗

PubMed2006

Characteristics of antiaromatic ring pi multi-hydrogen bonds in (H2O)n-C4H4 (n = 1, 2) complexes.

By counterpoise-corrected optimization method, the six antiaromatic ring pi multi-hydrogen bond structures with diversiform shapes for (H2O)n-C4H4 (n = 1,2) have been obtained at the MP2/aug-cc-pVDZ level. At the CCSD(T)/aug-cc-pVDZ level, the interaction energy obtained mainly depends on the numbers of H2O and fold numbers of the pi multi-hydrogen bond. The interaction energy order is -2.342 (1a with pi mono-hydrogen) < -2.777 (1b with pi bi-hydrogen) << -4.683 (2a with pi bi-hydrogen) < -4.734 (2b with pi tri-hydrogen) < -4.782 (2c with pi tri-hydrogen) < -5.009 kcal/mol (2d with pi tetra-hydrogen bond). Strangely, why is the interaction energy of the pi bi-hydrogen bond in 1b close to that of the pi mono-hydrogen bond in 1a (their difference is only 15.7%)? The reason is that a pi-type H-bond (as an accompanying interaction) between two lone pairs of the O-atom and a near pair of H-atoms of C4H4 exists shoulder by shoulder in structures 1a, 2a, 2b, and 2c and contributes to the interaction energy. Another accompanying interaction, a repulsive interaction between the pi H-bond (using the H-atom(s) of H2O) and the near pair of H-atoms of C4H4, is also found. For the structures and interaction energies, the pi-type H-bond produces four effects: bending the strong pi H-bond, attracting the pair of H-atoms of C4H4 so that they deviate from the C4 ring plane, showing the interaction energy contribution, and bringing the larger electron correlation contribution. The repulsive interaction also produces four effects: pushing the pair of H-atoms of C4H4 so that they deviate from its ring plane, elongating the distance of the pi H-bond, promoting the formation of pi-type H-bond, and slightly influencing the interaction energy. In the present paper, one C=C bond with two H2O (over and below the ring plane) forms a pi H-bond link in two ways: a strong-weak pi H-bond link and a strong-strong pi H-bond link. The stability contribution of the former is more favorable than the latter. One H2O forms a pi H-bond with C4H4 in two ways. One strong pi H-bond part (over or below the ring plane) always is accompanied by another H-bond part. The accompanying part is either a weak pi H-bond or pi-type H-bond.

Computer Simulation↗

PubMed2006

Novel superalkali superhalogen compounds (Li3)+(SH)- (SH=LiF2, BeF3, and BF4) with aromaticity: new electrides and alkalides.

Optimized structures, with all real frequencies, of superalkali superhalides (Li(3))(+)(SH)(-) (SH=LiF(2), BeF(3), and BF(4)), are obtained, for the first time, at the B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ computational levels. These superalkali superhalides possess three characteristics that are significantly different from normal alkali halides. 1) They have a variety of structures, which come from five bonding mode types: edge-face, edge-edge, face-face, face-edge, and staggered face-edge. We find that the bonding mode type closely correlates with the Li(3)-SH bond energy. 2) The valence electrons on the Li(3) ring are pushed out by the (SH)(-) anion, and become excess electrons, conferring alkalide or electride characteristics on these Li(3)-SH species, depending on the bonding mode type. 3) The highest occupied molecular orbital of each Li(3)-SH species is a doubly occupied delocalized sigma bonding orbital on the Li(3) ring, which indicates its aromaticity. It is noticeable that the maximum negative nucleus-independent chemical shift value (about -10 ppm) moves out from the center of the Li(3) ring, owing to repulsion by the SH(-) anion. We find that these superalkali superhalides are not only complicated "supermolecules", but are also a new type of alkalide or electride, with aromaticity.

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↗