Biomedical subjects

Qian Shu Li

Publications and source records attributed to Qian Shu Li.

At least 19 recordsLinked to original sources

PubMed2006

Ab initio study on the decomposition of first excited state HOOO radicals.

The HOOO radical plays a crucial role in atmospheric processes involving the OH radical and O(2) molecule. We present an ab initio molecular orbital theory study on the decomposition reaction of the first excited state HOOO((2)A') with respect to OH and O(2). The geometries and harmonic vibrational frequencies of all stationary points are calculated at the CASSCF and MRCI levels of theory in conjunction with the 6-31+G(d,p) basis set. The potential energy profile of the decomposition reaction is studied at the CASSCF/6-31+G(d,p) level of theory, in which the complete valence orbitals and electrons are included in the active space. The energies of the potential energy profile are further refined at the CASPT2 and MRCI levels of the theory. Additionally, we have determined the interesting reaction process: the HOOO((2)A') radical with C(s) symmetry does not dissociate to OH((2)Pi) and O(2)((3)Sigma(-)(g)) directly as this is forbidden by orbital symmetry, but dissociates to OH((2)Pi) and O(2)((3)Sigma(-)(g)) via the change in symmetry from C(s) to C(infinity v) symmetry with a low barrier.

Computer Simulation↗

PubMed2006

A DFT study on dinuclear metallocenes RMMR [R= (BCO)5, (BNN)5; M = Be, Mg, Ca, Zn, Cd].

A series of dinuclear metallocenes with formula RMMR [R= (BCO)5, (BNN)5; M = Be, Mg, Ca, Zn, Cd] are investigated via density functional theory. All these compounds contain two M[eta5-(BCO)5] fragments or two M[eta5-(BNN)5] fragments with a direct metal-metal single sigma bond. Detailed NBO analyses show that the metal-ligand interactions are predominantly ionic in nature and each metal atom is in its +1 oxidation state. NBO analyses indicate that the interaction between the B-B bonds and metal-metal antibond has played a role in the stabilities of these compounds.

Journal Article↗

PubMed2006

Direct dynamics study on the reaction of N2H4 with F atom: a hydrogen abstraction reaction?

We present a systematic direct ab initio dynamics investigation of the reaction between N2H4 and F atom, which is predicted to have three possible reaction channels. The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of all reaction channels were calculated at the UB3LYP/6-31+G(d,p) level of theory. Energetic information of stationary points and the points along the MEPs was further refined by means of the CCSD(T)/aug-cc-pVTZ method. The calculated results revealed that the first two primary channels (N2H4+F-->N2H3+HF) are equivalent and occur synchronously via the formation of a pre-reaction complex with Cs symmetry rather than via the direct H abstraction. The pre-reaction complex then evolves into a hydrogen-bonding intermediate through a transition state with nearly no barrier and a high exothermicity, which finally makes the intermediate further decompose into N2H3 and HF. Another reaction channel of minor role (N2H4+F-->NH2F+NH2) was also found during the calculations, which has the same Cs pre-reaction complex but forms NH2F and NH2 via another transition state with high-energy barrier and low exothermicity. The rate constants of these channels were calculated using the improved canonical variational transition state theory with the small-curvature tunneling correction (ICVT/SCT) method. The three-parameter ICVT/SCT rate constant expressions of k(ICVT/SCT) at the CCSD(T)/aug-cc-pVTZ//UB3LYP/6-31+G(d,p) level of theory within 220-3000 K were fitted as (7.64x10(-9))T (-0.87) exp(1180/T) cm3 mole-1 s-1 for N2H4+F-->N2H3+HF and 1.45x10(-12)(T/298)(2.17) exp(-1710/T) cm3 mole-1 s-1 for N2H4+F-->NH2F+NH2.

Journal Article↗

PubMed2006

Reaction-path dynamics and theoretical rate constants for the CH(n)F(4-n) + O3 --> HOOO + CH(n-1)F(4-n) (n = 2,3) reactions.

We present a theoretical study of the hydrogen abstraction reactions from CH(3)F and CH(2)F(2) by an ozone molecule. The geometries and harmonic vibrational frequencies of all stationary points are calculated at the MPW1K, BHandHLYP, and MPWB1K levels of theory. The energies of all of the stationary points were refined by using both higher-level (denoted as HL) energy calculations and QCISD(T)/6-311++G(2df,2pd) calculations based on the optimized geometries at the MPW1K/6-31+G(d,p) level of theory. The minimum energy paths (MEPs) were obtained by the MPW1K/6-31+G(d,p) level of theory. Energetic information of the points along the MEPs is further refined by the HL method. The rate constants were evaluated on the basis of the MEPs from the HL level of theory in the temperature range 200-2500 K by using the conventional transition-state theory (TST), the canonical variational transition-state theory (CVT), the microcanonical variational transition-state theory (microVT), the CVT coupled with the small-curvature tunneling (SCT) correction (CVT/SCT), and the microVT coupled with the Eckart tunneling correction (microVT/Eckart) based on the ab initio calculations. A general agreement was found among the TST, CVT, and microVT theories. The fitted three-parameter Arrhenius expressions of the calculated forward CVT/SCT and microVT/Eckart rate constants of the ozonolysis of fluoromethane are k(CVT/SCT)(T) = 2.76 x 10(-34)T(5.81)e((-13975/)(T)) and k(microVT/Eckart)(T) = 1.15 x 10(-34)T(5.97)e((-14530.7/)(T)), respectively. The fitted three-parameter Arrhenius expressions of the calculated forward CVT/SCT and microVT/Eckart rate constants of the ozonolysis of difluoromethane are k(CVT/SCT)(T) = 2.29 x 10(-36)T(6.42)e((-15451.6/)(T)) and k(microVT/Eckart)(T) = 1.31 x 10(-36)T(6.45)e((-15465.8/)(T)), respectively.

Journal Article↗

PubMed2006

Direct dynamics study on the hydrogen abstraction reactions N2H4 + R-->N2H3 + RH (R=NH2, CH3).

We present a direct ab initio dynamics study on the hydrogen abstraction reactions N(2)H(4)+R-->N(2)H(3)+RH (R=NH(2),CH(3)), which are predicted to have six possible reaction channels for NH(2) abstraction and four for CH(3) abstraction caused by the different N(2)H(4) isomers and various attacking orientations of foreign radical to N(2)H(4). The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of all reaction channels are obtained at the UMP2(full)6-31+G(d,p) level of theory. Energetic information of stationary points and the points along the MEPs is further refined by means of MC-QCISD method. The rate constants of these channels are calculated using the improved canonical variational transition-state theory with the small-curvature tunneling correction (ICVT/SCT) method. The calculated results show that the favorable reaction channels are channels (n1) and (n4) as well as (c1) and (c3) (refer to Scheme 1) in the whole temperature range. The total ICVT/SCT rate constants of all channels for the two reactions at the MC-QCISDUMP2(full)6-31+G(d,p) level are both in good agreement with the available experimental data, and corresponding three-parameter expressions of k(ICVTSCT) in 220-3000 K are fitted as 6.46 x 10(-15)(T298)(3.60) exp(-386T) cm(3) mol(-1) s(-1) for NH(2) abstraction and 1.04 x 10(-14)(T298)(4.00) exp(-2037T) cm(3) mol(-1) s(-1) for CH(3) abstraction. Additionally, the long range interaction between the H atom of X-H bond in foreign radicals and the lone pair on the nonreactive N atom of the transition states is further discussed to explain the various transition-state numbers of the two similar hydrogen abstraction reactions.

Journal Article↗

PubMed2006

Critical threshold of noise-induced energy transduction in molecular machinery system.

Responses of energy transduction of molecular machinery to random perturbation were investigated at the conditions where the system stayed near the bifurcation point. It was found that noise-induced oscillation (NIO) could occur. But how far from bifurcation point could one get the admissible region of NIO? We proposed and demonstrated numerically that there existed a critical threshold of NIO for each fixed noise intensity. Furthermore, it was found that noise intensity was a key factor for the determination of critical threshold. Finally, the detailed bifurcation diagram depending on noise intensity was replotted.

Journal Article↗

PubMed2006

Enhancement and sustainment of internal stochastic resonance in unidirectional coupled neural system.

In this study, the collective dynamical behavior of two unidirectionally, linearly coupled neurons was investigated. Our investigation illustrates that, depending on the coupling strength, the internal stochastic resonance (ISR) effect observed in one of the two neurons could be amplified or sustained by the other. The amplification of ISR is enhanced as the coupling strength is increased from 0. However, when the coupling strength is increased above a certain level, the amplification of ISR is reduced, implicating that there exists an optimal coupling strength for the information flow between two neurons. As the coupling strength is increased further, i.e., above the critical level, synchronization of the two subsystems is achieved, yet the two subsystems exhibit the same magnitude response to the external noise, suggesting that the information transmission among coupled subunits could not be improved by further enhancing their coupling strength. And similar phenomena could also be obtained for the nonidentical case.

Journal Article↗

PubMed2005

Direct dynamics study on the hydrogen abstraction reaction CH2O + HO2 --> CHO + H2O2.

We present a direct ab initio dynamics study on the hydrogen abstraction reaction CH2O + HO2 --> CHO + H2O2, which is predicted to have four possible reaction channels caused by different attacking orientations of HO2 radical to CH2O. The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of the four reaction channels are calculated at the B3LYP/cc-pVTZ level of theory. Energetic information of stationary points and the points along the MEPs is further refined by means of some single-point multilevel energy calculations (HL). The rate constants of these channels are calculated using the improved canonical variational transition-state theory with the small-curvature tunneling correction (ICVT/SCT) method. The calculated results show that, in the whole temperature range, the more favorable reaction channels are Channels 1 and 3. The total ICVT/SCT rate constants of the four channels at the HL//B3LYP/cc-pVTZ level of theory are in good agreement with the available experiment data over the measured temperature ranges, and the corresponding three-parameter expression is k(ICVT/SCT) = 3.13 x 10(-20) T(2.70) exp(-11.52/RT) cm3 mole(-1) s(-1) in the temperature range of 250-3000 K. Additionally, the flexibility of the dihedral angle of H2O2 is also discussed to explain the different experimental values.

Journal Article↗

PubMed2005

Mechanisms of difluoroethylene ozonolysis: a density functional theory study.

We present a density functional theory (DFT) study on the mechanisms of gas-phase ozonolysis of three isomers of difluoroethylene, namely, cis-1,2-difluoroethylene, trans-1,2-difluoroethylene, and 1,1-difluoroethylene. MPW1K/cc-pVDZ and BHandHLYP/cc-pVDZ methods are employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points were further refined at the QCISD(T)/cc-pVDZ and QCISD(T)/6-31+G(df,p) levels of theory with zero-point energy (ZPE) corrections. The ozone-cis-1,2-difluoroethylene reaction is predicted to be slower than the ozone-trans-1,2-difluoroethylene reaction. The enhanced reactivity of trans-1,2-difluoroethylene relative to the cis isomer is similar to the reactions of ozone with cis- and trans-dichloroethylene. The ozone-1,1-difluoroethylene reaction is predicted to be slower than the ozone-trans-1,2-difluoroethylene reaction. These results are in agreement with experimental studies. The calculated mechanisms indicate that in ozone-difluoroethylene reactions the yields of OH might be trivial, which is different from the reactions of ozone with unsaturated hydrocarbons.

Journal Article↗

PubMed2005

Density functional theoretical study of a series of binary azides M(N3)n (n = 3, 4).

Geometrical structures of a series of binary azides M(N3)n (M = elements in groups 3 and 13 (n = 3) and in groups 4 and 14 (n = 4)) were investigated at the B3LYP/6-311+G level of theory. Our calculations found that binary group 3 triazides M(N3)3 (M = Sc, Y, La) and binary group 4 tetraazides M(N3)4 (M = Ti, Zr, Hf) turn out to be stable with all frequencies real having a similar linear M-N-NN structural feature, as previously reported for M(N3)4 (M = Ti, Zr, Hf). However, binary azides of group 13 M(N3)3 (M = B, Al, Ga, In, Tl) and group 14 elements M(N3)4 (C, Si, Ge, Sn, Pb) with bent M-N-NN bond angles differ obviously from binary group 3 and 4 azides in geometrical structure. These facts are mainly explained by the difference in electronic density overlap between the central atom and the alpha-N atoms of the azido groups. Two lone-pair electrons on the sp hybridization alpha-N atoms in the binary group 3 and 4 azides donate electron density into two empty d orbitals of the central transition metal atom and a pair of valence bonding electrons, resulting in the alpha-N atoms acting as a tridentate ligand. The sp2 hybridization alpha-N atoms of the binary group 13 and 14 azides only give one valence electron to form one valence bonding electron pair acting virtually as monodentate donors.

Journal Article↗

PubMed2005

Turing pattern formation in coupled reaction-diffusion system with distributed delays.

Turing pattern formation in coupled two-layer system with distributed delayed is investigated. Numerical simulations prove that, when the coupling is weak, it can apparently accelerate the formation process and enhance the spatial amplitude of the pattern. When it is strong, it will prolong the formation process or even inhibit the pattern and turn the whole system into bulk oscillatory state by its influence on the transient oscillatory state. If the coupling covers only part of the system, Turing pattern can be prominently oriented according to the shape of the coupling area at tiny coupling strength. However, if the coupling is too strong, the Turing pattern may also be destroyed. This means that in coupled systems, the delay effect in the cross-layer signal transfer may significantly influence the spatial character and/or the evolution dynamics in Turing pattern formation, even to destroy the pattern. This work is of practical significance in the study of Turing pattern in biosystems, where bilayer membranes or multilayer tissues are often found.

Chemistry, Physical↗

PubMed2005

The reaction of the aminoboranylidene-iminoborane isomerization: a CASSCF direct dynamics study.

The barrier and the potential-energy surface of the isomerization from aminoboranylidene (BNH2) to iminoborane (HBNH) have been studied using complete active space self-consistent field (CASSCF) with the 6-31 + G(d, p) basis set and higher-level energy methods. The rate constants of the isomerization reaction are reported by employing the direct ab initio dynamics method. The geometries of all the stationary points were optimized using the B3LYP and CCSD methods with the cc-pVTZ and cc-pVQZ basis sets. The information along the intrinsic reaction coordinate (IRC) was also calculated at the CASSCF/6-31 + G (d,p) level of theory. The energies were refined at the G3, G3MP2, G3MP2B3, CBS-Q, CBS-QB3, and two high-level (HL) methods based on the geometries optimized using CASSCF/6-31 + G(d,p). The rate constants were evaluated using conventional transition-state theory (TST), canonical variational transition-state theory (CVT), and canonical variational transition-state theory with small curvature tunneling correction (CVT/SCT) and conventional transition-state theory with Eckart tunneling correction (TST/Eckart). According to the calculated results, we conclude that the tunneling effect is very important to this isomerization reaction.

Boranes↗

PubMed2005

N4 ring as a square planar ligand in novel MN4 species.

Ab initio (MP2) and density functional theory (DFT) methods are used to examine a series of MN4 compounds, where M is an alkaline-earth cation (Mg2+, Ca2+, Sr2+, Ba2+), and N4(2-) is a six--electron ring. All pyramidal structures except MgN4 are the most energetically favored for all singlet MN4 systems considered here. For MgN4, the CS structure with dicoordinated Mg out of the N4 ring plane is the most stable of all. Among these systems, the pyramidal CaN4, SrN4, BaN4 and the planar C(S) structure containing dicoordinated Ba are stable as singlet molecules due to their significant isomerization or dissociation barriers (21.3-94.1 kcal/mol). Structural, natural bond orbital (NBO), and molecular orbital (MO) analyses indicate that the bonding in the BaN4 system has a larger covalent character as compared with other MN4 systems. In addition, substantial d character is found in the bonding of the MN4 (M = Ca2+, Sr2+, Ba2+) species.

Journal Article↗

PubMed2004

Direct ab initio dynamics studies of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical.

The kinetics of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical were studied using the direct ab initio dynamics approach. BHandHLYP/cc-pVDZ method was employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points for the two reactions were further refined at the QCISD(T)/cc-pVTZ level of theory. No barrier was found at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory for both reactions. The forward and reverse rate constants were evaluated with both canonical variational transition state theory (CVT) and microcanonical variational transition state theory (mu VT) in the temperature range of 300-2,500 K. The fitted three-parameter Arrhenius expression of the calculated CVT rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory are k(CVT) (n-C3H7) = 1.68 x 10(-14) T(0.84) e((319.5/T)) cm3 molecule(-1) s(-1) and k(CVT) (iso-C3H7)=4.99 x 10(-14) T(0.90) e((159.5/T)) cm3 molecule(-1) s(-1) for reactions of n-C3H7 + H and iso-C3H7 + H, respectively, which are in good agreement with available literature data. The variational effects were analysed.

Alkenes↗

PubMed2004

Direct ab initio dynamics study on the rate constants and kinetics isotope effects of CH(3)O+H-->CH(2)O+H(2) reaction.

We present a direct ab initio dynamics study of thermal rate constants of the hydrogen abstraction reaction of CH(3)O+H-->CH(2)O+H(2). The unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set, the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set, and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set methods were employed to optimize the structures and to calculate frequencies for all stationary points. Minimum energy paths were obtained by the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional and the unrestricted quadratic configuration interaction calculation including single and double substitutions with the same Dunning's correlation consistent polarized valence double-zeta basis set levels of theory. No barrier is found at the unrestricted Becke's half-and-half hybrid functional using the Lee-Yang-Parr correlation functional with Dunning's correlation consistent polarized valence double-zeta basis set level of theory in contrast to a small barrier of 1.43 kcal mol(-1) at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory. In particular, the barrier vanishes as the energies along the minimum energy path MEP are refined at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set level of theory. Smaller barriers of 0.47 and 0.17 kcal mol(-1) were obtained at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set and the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence triple-zeta basis set levels of theory, respectively. The forward rate constants are evaluated with the canonical variational transition state theory in the temperature range of 300-2500 K. The calculated forward rate constants at the unrestricted quadratic configuration interaction calculation including single and double substitutions with a triples contribution with Dunning's correlation consistent polarized valence triple-zeta basis set based on the geometries at the unrestricted quadratic configuration interaction calculation including single and double substitutions with Dunning's correlation consistent polarized valence double-zeta basis set level of theory are in good agreement with the available experimental data. The kinetic isotope effects are estimated.

Journal Article↗

PubMed2004

Controlling of explicit internal signal stochastic resonance by external signal.

Explicit internal signal stochastic resonance (EISSR) is investigated in a model of energy transduction of molecular machinery when noise is added to the region of oscillation in the presence of external signal (ES). It is found that EISSR could be controlled, i.e., enhanced or suppressed by adjusting frequency (omega(e)) and amplitude (A) of ES, and that there exits an optimal frequency for ES, which makes EISSR strength reach the maximum. Meanwhile, a critical amplitude (A(c)) is found, which is a threshold of occurrence of EISSR. Finally, the difference and similarity between EISSR and IISSR (implicit internal signal stochastic resonance) are discussed.

Journal Article↗

PubMed2004

Control of Turing pattern by weak spatial perturbation.

The control of Turing pattern formation by weak spatial perturbation is investigated. The weak spatial perturbation added before Turing pattern stabilization is found to show prominent spatial orientation effect. The control process of perturbation to Turing patterns is tracked. The effect of perturbation factors, such as amplitude and imposing time are also discussed.

Journal Article↗

PubMed2004

Internal stochastic resonance under two-parameter modulation in intercellular calcium ion oscillations.

Internal stochastic resonance (ISR) in a model of intercellular calcium ion oscillations is investigated under the modulation of two parameters, viz., degree of extracellular stimulation (beta) and leak rate (k(f)). ISR can occur when either beta or k(f) is subjected to a noise. Internal stochastic biresonance (ISBR) can occur when noise is added to the two parameters simultaneously. The distance to the bifurcation point is found to be able to enhance or suppress the ISBR, and to affect the number of peaks of ISR.

Journal Article↗