Biomedical subjects

Soo-Y Lee

Publications and source records attributed to Soo-Y Lee.

8 recordsLinked to original sources

PubMed2006

A test of the continuous configuration time-dependent self-consistent field (CC-TDSCF) method on the H + CH4 reaction.

The continuous configuration time-dependent self-consistent field (CC-TDSCF) method is employed to calculate the flux-flux autocorrelation functions for the H + CH4 reaction on the potential energy surface recently developed by Manthe and co-workers. We include up to 10 out of the total 12 degrees of freedom in our calculations, only with the doubly degenerate bending modes involving the motion of the hydrogens in nonreacting CH3 group excluded. Comparison of flux-flux autocorrelation functions obtained by using the exact dynamics method and the CC-TDSCF method shows that the CC-TDSCF method is capable of producing very accurate results. Our calculations clearly reveal that the CC-TDSCF method is a powerful approximation quantum dynamics method. It allows us to partition a big problem into several smaller ones. By changing partition systematically, one can investigate the correlations between different degrees of freedom. By grouping modes with strong correlations together as a cluster, one can systematically improve accuracy of the result.

Computer Simulation↗

PubMed2006

A full dimensional time-dependent wave packet study for the H4 four-center, collision induced dissociation, and single exchange reactions: reaction probabilities for J=0.

A time-dependent initial state selected wave packet method has been developed to study the H2(v(1)=10-11,j1=0)+H2'(v2=0,j2=0)-->HH'+HH' four-center (4C) reaction, and two other competing reactions: the H2+H2'-->H+H+H2' collision induced dissociation (CID) and the H2+H2'-->H+HH'+H' single exchange (SE) reaction, in full six dimensions. Initial state-specific total reaction probabilities for these three competing reactions are presented for total angular momentum J=0 and the effects of reagent vibration on reactions are examined. It is found that (a) the CID process is the dominant process over the whole energy range considered in this study, but the 4C and SE processes also have non-negligible probabilities; (b) the SE process has a lower threshold energy than the 4C process, but the SE probability increases slower than the 4C probability as collision energy increases; (c) the vibrational excitation of H2(v1) is much more efficient than translational motion for promoting these processes, in particular to the CID process.

Journal Article↗

PubMed2005

Continuous configuration time-dependent self-consistent field method for polyatomic quantum dynamical problems.

A new continuous configuration time-dependent self-consistent field method has been developed to study polyatomic dynamical problems by using the discrete variable representation for the reaction system, and applied to a reaction system coupled to a bath. The method is very efficient because the equations involved are as simple as those in the traditional single configuration approach, and can account for the correlations between the reaction system and bath modes rather well.

Journal Article↗

PubMed2005

Dependence of line shapes in femtosecond broadband stimulated Raman spectroscopy on pump-probe time delay.

The effect of the time delay between the picosecond Raman pump and the femtosecond Stokes probe pulse on the Raman gain line shape in femtosecond broadband stimulated Raman spectroscopy (FSRS) is presented. Experimental data are obtained for cyclohexane to investigate the dependence of the FSRS line shape on this time delay. Theoretical simulations of the line shapes as a function of the time delay using the coupled wave theory agree well with experimental data, recovering broad line shapes at positive time delays and narrower bands with small Raman loss side wings at negative time delays. The analysis yields the lower bounds of the vibrational dephasing times of 2.0 ps and 0.65 ps for the 802 and 1027 cm(-1) modes for cyclohexane, respectively. The theoretical description and simulation using the coupled wave theory are also consistent with the observed Raman gain intensity profile over time delay, reaching the maximum at a slightly negative time delay (approximately -1 ps), and show that the coupled wave theory is a good model for describing FSRS.

Journal Article↗

PubMed2004

Theory of femtosecond stimulated Raman spectroscopy.

Femtosecond broadband stimulated Raman spectroscopy (FSRS) is a new technique that produces high-resolution (time-resolved) vibrational spectra from either the ground or excited electronic states of molecules, free from background fluorescence. FSRS uses simultaneously a narrow bandwidth approximately 1-3 ps Raman pump pulse with a continuum approximately 30-50 fs Stokes probe pulse to produce sharp Raman gains, at positions corresponding to vibrational transitions in the sample, riding on top of the continuum Stokes probe spectrum. When FSRS is preceded by a femtosecond actinic pump pulse that initiates the photochemistry of interest, time-resolved Raman spectroscopy can be carried out. We present two theoretical approaches to FSRS: one is based on a coupling of Raman pump and probe light waves with the vibrations in the medium, and another is a quantum-mechanical description. The latter approach is used to discuss the conditions of applicability and limitations of the coupled-wave description. Extension of the quantum-mechanical description to the case where the Raman pump beam is on resonance with an excited electronic state, as well as when FSRS is used to probe a nonstationary vibrational wave packet prepared by an actinic pump pulse, is also discussed.

Journal Article↗

PubMed2002

State-to-State integral cross section for the H+H2O-->H2+OH abstraction reaction.

The initial state selected time-dependent wave-packet method was extended to calculate the state-to-state integral cross section for the title reaction with H2O in the ground rovibrational state on the potential energy surface of Yang, Zhang, Collins, and Lee. One OH bond length was fixed in the study, which is justifiable for the abstraction reaction, but the remaining 5 degrees of freedom were treated exactly. It was found that the H2 molecule is produced vibrationally cold for collision energy up to 1.6 eV. The OH rotation takes away about 4% of total available energy in the products, while the fraction of energy going to H2 rotation increases with collision energy to about 20% at 1.6 eV.

Journal Article↗

PubMed2002

Probing the transition state via photoelectron and photodetachment spectroscopy of H(3)O(-).

The H(3)O(-) anion has stable and metastable structures that resemble configurations in the vicinity of the transition state for the neutral reactions OH + H(2) <--> H(2)O + H. Photoelectron spectroscopy of this anion probes the neutral reaction dynamics in the critical transition-state region. Accurate quantum dynamics calculations of the photoelectron intensity and photodissociation product energies are shown to provide a quantitatively reliable means of interpreting such experimental observations and reveal a detailed picture of the reaction dynamics.

Journal Article↗

PubMed2002

Breakdown of the spectator model for the OH bonds in studying the H+H2O reaction.

The time-dependent wave packet method is used to study the exchange and abstraction processes for the H+H2O reaction with both OH bonds in the H2O reactant treated as reactive bonds in full dimension. The calculation clearly shows that it is necessary to treat both OH bonds in this way in order to accurately investigate the exchange process. However, for the abstraction process, the spectator model works very well. Nonreactive treatment of one OH bond by using a few vibrational basis functions or even freezing the bond can yield very accurate abstraction reaction probability.

Journal Article↗