Browsing by Author "Lin, Sheng-Hsien"

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Anharmonic Effect of N-Propyl Peroxy Dissociation
(2016-12)
Song, Liguo
;
Pan, Xinxiang
;
Li, Qian
;
Ding, Yang
;
Yao, Li
The anharmonic and harmonic dissociation rate constants of alkylperoxy (RO2) in different pathways, as well as those for the reactions of the n-propyl peroxy radical, were calculated using the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. When the temperature/total energy increased, the rate constants of the different pathways varied independently, causing changes in the dominating/leading products. Anharmonic rate constants were larger than harmonic rate constants, and their difference increased with increasing temperature/energy. Therefore, the anharmonic effect cannot be neglected. The rate-determining steps of CH3CH2CH2OO dissociation are discussed. Then the anharmonic effect was found clearly for CH3CH2CH2OO dissociation, especially for the hydroperoxyalkyl radical (QOOH) dissociation. At low temperature, the rate constants were similar to those found from experiment, which indicated the RRKM theory was suitable for calculating the dissociation rates of RO2 species.
Anharmonic Effect of N-Propyl Peroxy Dissociation
(2016-12)
Song, Liguo
;
Pan, Xinxiang
;
Li, Qian
;
Ding, Yang
;
Yao, Li
The anharmonic and harmonic dissociation rate constants of alkylperoxy (RO2) in different pathways, as well as those for the reactions of the n-propyl peroxy radical, were calculated using the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. When the temperature/total energy increased, the rate constants of the different pathways varied independently, causing changes in the dominating/leading products. Anharmonic rate constants were larger than harmonic rate constants, and their difference increased with increasing temperature/energy. Therefore, the anharmonic effect cannot be neglected. The rate-determining steps of CH3CH2CH2OO dissociation are discussed. Then the anharmonic effect was found clearly for CH3CH2CH2OO dissociation, especially for the hydroperoxyalkyl radical (QOOH) dissociation. At low temperature, the rate constants were similar to those found from experiment, which indicated the RRKM theory was suitable for calculating the dissociation rates of RO2 species.
Anharmonic Rice-Ramsperger-Kassel-Marcus (RRKM) and product branching ratio calculations for the partially deuterated protonated water dimers: Dissociation and isomerization
(2013-03-14)
Song, Di
;
Su, Hongmei
;
Kong, Fan-ao
;
Lin, Sheng-Hsien
;
應用化學系分子科學碩博班
Partially deuterated protonated water dimers, H2O center dot H+ center dot D2O, H2O center dot D+ center dot HDO, and HDO center dot H+ center dot HDO, as important intermediates of isotopic labeled reaction of H3O+ + D2O, undergo direct dissociation and indirect dissociation, i.e., isomerization before the dissociation. With Rice-Ramsperger-Kassel-Marcus theory and ab initio calculations, we have computed their dissociation and isomerization rate constants separately under the harmonic and anharmonic oscillator models. On the basis of the dissociation and isomerization rate constants, branching ratios of two primary products, [HD2O+]/[H2DO+], are predicted under various kinetics models with the harmonic or anharmonic approximation included. The feasible kinetics model accounting for experimental results is shown to include anharmonic effect in describing dissociation, while adopting harmonic approximation for isomerization. Thus, the anharmonic effect is found to play important roles affecting the dissociation reaction, while isomerization rates are shown to be insensitive to whether the anharmonic or harmonic oscillator model is being applied. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4794152]
Anharmonic RRKM Calculation for the Dissociation of (H(2)O)(2)H(+) and Its Deuterated Species (D(2)O)(2)D(+)
(2010-09-23)
Song, Di
;
Su, Hongmei
;
Kong, Fan-ao
;
Lin, Sheng-Hsien
;
應用化學系分子科學碩博班
Investigations on the dissociation kinetics of hydrated protonium ions, (H(2)O)(2)H(+) and their deuterated species (H(2)O)(2)D(+), are reported based on the harmonic and anharmonic oscillator model using the transition state theory and ab initio calculations. We find that the dissociation of (H(2)O)(2)H(+) and (D(2)O)(2)D(+) exhibits a distinct threshold behavior due to the existence of activation energies. Moreover, the deviation between the harmonic and anharmonic dissociation rate constants becomes larger in the high energy or temperature range, with the rate constants becoming unreasonably large under the harmonic oscillator model. The isotope effect is found to become more distinct but only in the case of the anharmonic oscillator model. These results show that the anharmonic Rice-Ramsperger-Kassel-Marcus (RRKM) theory can provide a reasonably good description for the dissociation of (H(2)O)(2)H(+) and (D(2)O)(2)D(+). Furthermore, a theoretical model to demonstrate the principle of vibrational predissociation spectroscopy (VPS) is established from the viewpoint of RRKM theory and applied in determining the experimental conditions and understanding the role of the dissociation rate constant k(E) played in the VPS experiment, using (H(2)O)(2)H(+) and (H(2)O)(2)D(+) as examples.
Anharmonic RRKM Calculation for the Dissociation of (H2O)(2)H+ and Its Deuterated Species (D2O)(2)D+
(2010-09-23)
Song, Di
;
Su, Hongmei
;
Kong, Fan-ao
;
Lin, Sheng-Hsien
;
應用化學系分子科學碩博班
Investigations on the dissociation kinetics of hydrated protonium ions, (H2O)(2)H+ and their deuterated species (H2O)(2)D+, are reported based on the harmonic and anharmonic oscillator model using the transition state theory and ab initio calculations. We find that the dissociation of (H2O)(2)H+ and (D2O)(2)D+ exhibits a distinct threshold behavior due to the existence of activation energies. Moreover, the deviation between the harmonic and anharmonic dissociation rate constants becomes larger in the high energy or temperature range, with the rate constants becoming unreasonably large under the harmonic oscillator model. The isotope effect is found to become more distinct but only in the case of the anharmonic oscillator model. These results show that the anharmonic Rice-Ramsperger-Kassel-Marcus (RRKM) theory can provide a reasonably good description for the dissociation of (H2O)(2)H+ and (D2O)(2)D+. Furthermore, a theoretical model to demonstrate the principle of vibrational predissociation spectroscopy (VPS) is established from the viewpoint of RRKM theory and applied in determining the experimental conditions and understanding the role of the dissociation rate constant k(E) played in the VPS experiment, using (H2O)(2)H+ and (H2O)(2)D+ as examples.
Constraint Trajectory Surface-Hopping Molecular Dynamics Simulation of the Photoisomerization of Stilbene
(2014)
Lei, Yibo
;
Wu, Shaomei
;
Zhu, Chaoyuan
;
Wen, Zhenyi
;
Lin, Sheng-Hsien
Combining trajectory surface hopping (TSH) method with constraint molecular dynamics, we have extended TSH method from full to flexible dimensional potential energy surfaces. Classical trajectories are carried out in Cartesian coordinates with constraints in internal coordinates, while nonadiabatic switching probabilities are calculated separately in free internal coordinates by Landau-Zener and Zhu-Nakamura formulas along the seam. Two-dimensional potential energy surfaces of ground S-0 and excited S-1 states are constructed analytically in terms of torsion angle and one dihedral angle around the central ethylenic C-C bond, and the other internal coordinates are all fixed at configuration of the conical intersection. At this conical intersection, the branching ratio from the present simulation is 48 : 52 (33 : 67) initially starting from trans(cis)-Stilbene in comparison with experimental value 50 : 50. Quantum yield for trans-to-cis isomerization is estimated as 49% in very good agreement with experimental value of 55%, while quantum yield for cis-to-trans isomerization is estimated as 47% in comparison with experimental value of 35%.
Exploration of hydrogen bond networks and potential energy surfaces of methanol clusters using a two-stage clustering algorithm
(2017)
Hsu, Po-Jen
;
Ho, Kun-Lin
;
Lin, Sheng-Hsien
;
Kuo, Jer-Lai
;
應用化學系
The potential energy surface (PES), structures and thermal properties of methanol clusters (MeOH)(n) with n = 8-15 were explored by replica-exchange molecular dynamics (REMD) simulations with an empirical model and refined using density functional theory (DFT) methods. For a given size, local minima structures were sampled from REMD trajectories and archived by a newly developed molecular database via a two-stage clustering algorithm (TSCA). Our TSCA utilizes both the topology of O-H center dot center dot center dot O hydrogen bonding networks and the similarity of the shapes to filter out duplicates. The screened molecular database contains only distinct conformers sampled from REMD and their structures are further optimized by the two DFT methods with and without dispersion correction to examine the influence of dispersion on their structures and binding energies. Inspecting different O-H center dot center dot center dot O networks, the binding energies of methanol clusters are highly degenerated. The degeneracy is more significant with the dispersion effect that introduces weaker but more complex C-H center dot center dot center dot O bonds. Based on the structures we have searched, we were able to extract general trends and these datasets can serve as a starting point for further high-level ab initio calculations to reveal the true energy landscape of methanol clusters.
Folding Thermodynamics of a Beta-Hairpin Peptide: A Theoretical Study
(2012-01-31)
Tsai, Min-Yeh
;
Yuan, Jian-Min
;
Teranishi, Yoshiaki
;
Lin, Sheng-Hsien
;
交大名義發表
Franck-Condon factors perturbed by damped harmonic oscillators: Solvent enhanced X (1)A(g) <-> A(1)B(1u) absorption and fluorescence spectra of perylene
(2014-08-28)
Wang, Chen-Wen
;
Yang, Ling
;
Zhu, Chaoyuan
;
Yu, Jian-Guo
;
Lin, Sheng-Hsien
Damped harmonic oscillators are utilized to calculate Franck-Condon factors within displaced harmonic oscillator approximation. This is practically done by scaling unperturbed Hessian matrix that represents local modes of force constants for molecule in gaseous phase, and then by diagonalizing perturbed Hessian matrix it results in direct modification of Huang-Rhys factors which represent normal modes of solute molecule perturbed by solvent environment. Scaling parameters are empirically introduced for simulating absorption and fluorescence spectra of an isolated solute molecule in solution. The present method is especially useful for simulating vibronic spectra of polycyclic aromatic hydrocarbon molecules in which hydrogen atom vibrations in solution can be scaled equally, namely the same scaling factor being applied to all hydrogen atoms in polycyclic aromatic hydrocarbons. The present method is demonstrated in simulating solvent enhanced X (1)A(g) <-> A(1)B(1u) absorption and fluorescence spectra of perylene (medium-sized polycyclic aromatic hydrocarbon) in benzene solution. It is found that one of six active normal modes v10 is actually responsible to the solvent enhancement of spectra observed in experiment. Simulations from all functionals (TD) B3LYP, (TD) B3LYP35, (TD) B3LYP50, and (TD) B3LYP100 draw the same conclusion. Hence, the present method is able to adequately reproduce experimental absorption and fluorescence spectra in both gas and solution phases. (C) 2014 AIP Publishing LLC.
Franck-Condon simulation for unraveling vibronic origin in solvent enhanced absorption and fluorescence spectra of rubrene
(2017)
Hu, Ying
;
Wang, Chen-Wen
;
Zhu, Chaoyuan
;
Gu, Fenglong
;
Lin, Sheng-Hsien
Quantum chemistry calculations at the level of (TD)-DFT plus PCM solvent models are employed for analyzing potential energy surfaces and as a result two local minima with D-2, two local minima with C-2H, and one second-order transition state with D-2H group symmetry are found in both ground S-0 and excited-state S-1 potential energy surfaces. Simulated vibronic coupling distributions indicate that only second-order transition states with D-2H group symmetry are responsible for observed absorption and fluorescence spectra of rubrene and vibrational normal-motions related with atoms on the aromatic backbone are active for vibronic spectra. The Stokes shift 1120 cm(-1) (820 cm(-1)) and vibronic-band peak positions in both absorption and fluorescence spectra in non-polar benzene (polar cyclohexane) solvent are well reproduced within the conventional Franck-Condon simulation. By adding damped oscillator correction to Franck-Condon simulation, solvent enhanced vibronic-band intensities and shapes are well reproduced. Four (three) normal modes with vibration frequency around 1550 cm(-1) (1350 cm(-1)) related to ring wagging plus CC stretching and CH bend motions on the backbone are actually interpreted for solvent enhanced absorption (fluorescence) spectra of rubrene in benzene and cyclohexane solutions.
Franck-Condon simulation for unraveling vibronic origin in solvent enhanced absorption and fluorescence spectra of rubrene
(2017-01-01)
Hu, Ying
;
Wang, Chen-Wen
;
Zhu, Chaoyuan
;
Gu, Fenglong
;
Lin, Sheng-Hsien
Quantum chemistry calculations at the level of (TD)-DFT plus PCM solvent models are employed for analyzing potential energy surfaces and as a result two local minima with D-2, two local minima with C-2H, and one second-order transition state with D-2H group symmetry are found in both ground S-0 and excited-state S-1 potential energy surfaces. Simulated vibronic coupling distributions indicate that only second-order transition states with D-2H group symmetry are responsible for observed absorption and fluorescence spectra of rubrene and vibrational normal-motions related with atoms on the aromatic backbone are active for vibronic spectra. The Stokes shift 1120 cm(-1) (820 cm(-1)) and vibronic-band peak positions in both absorption and fluorescence spectra in non-polar benzene (polar cyclohexane) solvent are well reproduced within the conventional Franck-Condon simulation. By adding damped oscillator correction to Franck-Condon simulation, solvent enhanced vibronic-band intensities and shapes are well reproduced. Four (three) normal modes with vibration frequency around 1550 cm(-1) (1350 cm(-1)) related to ring wagging plus CC stretching and CH bend motions on the backbone are actually interpreted for solvent enhanced absorption (fluorescence) spectra of rubrene in benzene and cyclohexane solutions.
Global and Local Structural Changes of Protein Unfolding
(2009)
Shiu, Ying-Jen
;
Jeng, U-Ser
;
Lin, Sheng-Hsien
;
應用化學系
;
應用化學系分子科學碩博班
In the mean-field Ising model, the folding-unfolding behavior of a protein is regarded as an ensemble of units reduced from, presumably, peptide bonds or amino acid residues. Units of similar thermodynamic properties are further classified into groups that are related to, for instance, alpha-helices or beta-sheets. Units of the same group are assumed to unfold collectively, whereas those of different groups may undergo either sequential or coupled unfolding. The introduction of unfolding groups facilitates the description of non-collective local structural changes experimentally observed via a multi-group unfolding. We incorporate denaturants and temperature effects into the free energy expression of the protein upon dissolution in a specific environment at thermal equilibrium, and a model protein, cytochrome c, was examined. Results indicate that there are at least four unfolding groups induced unfolding of cytochrome c: two are related to the prosthetic heme group, whereas another two groups are a-helices and global nearly group, which largely account for global changes in protein morphology. The extracted thermodynamic parameters, on the basis of the Ising model, can closely predict unfolding behaviors of the proteins in compounded denaturing environments.
Intersystem Crossing Pathway in Quinoline-Pyrazole Isomerism: A Time-Dependent Density Functional Theory Study on Excited-State Intramolecular Proton Transfer
(2015-06-18)
Liu, Yu-Hui
;
Lan, Sheng-Cheng
;
Zhu, Chaoyuan
;
Lin, Sheng-Hsien
;
應用化學系分子科學碩博班
The dynamics of the excited-state intramolecular proton-transfer (ESIPT) reaction of quinoline pyrazole (QP) isomers, designated as QP-I and QP-II, has been investigated by means of time-dependent density functional theory (TDDFT). A lower barrier has been found in the potential energy curve for the lowest singlet excited state (S-1) along the proton-transfer coordinate of QP-II compared with that of QP-I; however, this is at variance with a recent experimental report [J. Phys. Chem. A 2010, 114, 7886-7891], in which the authors proposed that the ESIPT reaction would only proceed in QP-I due to the absence of a PT emission for QP-II. Therefore, several deactivating pathways have been investigated to determine whether fluorescence quenching occurs in the PT form of QP-II (PT-II). The Si state of PT-II has n pi* character, which is a well-known dark state. Moreover, the energy gap between the S-1 and T-2 states is only 0.29 eV, implying that an intersystem crossing (ISC) process would occur rapidly following the ESIPT reaction. Therefore, it is demonstrated that the ESIPT could successfully proceed in QP-II and that the PT emission would be quenched by the ISC process.
Intrinsic coordination for revealing local structural changes in protein folding-unfolding
(2016-01-28)
Shiu, Ying-Jen
;
Hayashi, Michitoshi
;
Shih, Orion
;
Su, Charlene
;
Tsai, Min-Yeh
With a deformed object of a rigid rod inside, the local dislocations may be tracked relatively easily with respect to the internal rigid rod. We apply this concept on protein folding-unfolding to track the internal structural changes of an unfolded protein in solution. Proposed here is a protein internal coordination based on the major axis X of an ellipsoidal protein and the stable intrinsic transition dipole moment mu of the protein during unfolding. In this methodology, small-angle X-ray scattering (SAXS) is used to provide the protein global morphologies in the native and unfolded states. Furthermore, time-resolved fluorescence anisotropy (TRFA) provides the relative orientation between X and mu of Trp59 of the model protein cytochrome c. Hence observed in the protein unfolding with denaturants, acid, urea, or GuHCl, is the elongation of the native protein conformation along a reoriented protein major axis; accompanied are the different extents of relocations of the terminal a helices and loop structures of the protein in the corresponding unfolding.
Kinetic Ising Model Study of Protein Aggregation
(2014-01-28)
Tsai, Min-Yeh
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Yuan, Jian-Min
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Lin, Sheng-Hsien
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應用化學系
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Department of Applied Chemistry
Magnetism-tuning strategies for graphene oxide based on magnetic oligoacene oxide patches model
(2018-02-07)
Wen, Yanjie
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Yen, Chia-Liang
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Yan, Linyin
;
Kono, Hirohiko
;
Lin, Sheng-Hsien
Graphene oxide (GO) has wide application potential owing to its 2D structure and diverse modification sites for various targeted uses. The introduction of magnetism into GO structures has further advanced the controllability of the application of GO materials. Herein, the concept of modular design and modeling was applied to tune the magnetism of GO. To obtain desirable magnetic properties, diradicalstructured GO patches were formed by the introduction of two functional groups to break the Kekule structure of the benzene ring. In these diradical GO patches, the energy of the triplet state was lower than those of the open-shell broken-symmetry singlet state and closed-shell singlet state. To create such multi-radical patches, a practical approach is to determine a substantial spatial separation of the alpha and beta spin densities in the molecule. Thus, systematic design strategies and tests were evaluated. The first strategy was extending the distance between the distribution center of the alpha and beta spin densities; the second was controlling the delocalization directions of the alpha and beta electrons; the third was controlling the delocalization extension of the alpha and beta electrons by oxidative modification, and finally introducing multi-radical structures into the molecular system and controlling the position of each radical. Herein, successful paves the way to explore ferromagnetic MGO guided by theoretical study, which may become reality soon.
Neutral Dissociation of Superexcited Oxygen Molecules in Intense Laser Fields
(2010-03-11)
Song, Di
;
Azarm, Ali
;
Kamali, Yousef
;
Liu, Kai
;
Xia, Andong
Superexcited States (SESs) of oxygen molecules and their neutral dissociation processes have been studied both experimentally and theoretically using intense femtosecond laser. We find that at the laser Intensity of similar to 2 x 10(14) W/cm(2), ultrashort laser pulse causes neutral dissociation of oxygen molecule by way of SESs. The dissociation products are the excited neutral oxygen atoms, which are observed that fluorescence,Spectroscopy. Laser power dependence of the fluorescence intensity shows that each molecule effectively absorbs ill average of tell laser photons. The total energy absorbed is sufficient to stimulate the molecule to many of the SESs The effect is equivalent to single photon excitation in the extreme-ultraviolet (XUV) region by synchrotron radiation (SR). Morse potential energy curves (PECs). are constructed for the SESs of O(2) molecules. In light of the PECs, predissociation mechanism is proposed for the neutral dissociation. Quasi-classical trajectroy (QCT) calculations show that the predissociation time is as short as 100 fs, which is consistent with our experimental measurement using ultrafast pump-probe technique
On the calculation of rate constants of the small cyclic water cluster by anharmonic RRKM theory
(2009-08-27)
Shao, Ying
;
Yao, Li
;
Lin, Sheng-Hsien
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應用化學系
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Department of Applied Chemistry
The rate constants for concerted exchange reaction of the small cyclic water clusters (H(2)O)(n)(3, 4) were calculated with the YL method. The anharmonic effect on the concerted hydrogen exchange reaction was examined. For the trimer water, at temperature 300 K, the anharmonic rate constant is k 4: 70 x 10(-4) s(-1), and for the tetramer water, the value is 0: 55 s(-1). The tunneling effect is very small for this two concerted hydrogen exchange reactions and can be neglected in the two reactions. The results are in reasonable agreement with the value given by Loerting et al. Besides that, the anharmonic effect is not significant for the concerted hydrogen exchange reaction of (H(2)O)(n)(3, 4). (C) 2009 Elsevier B. V. All rights reserved.
Orientation hydrogen-bonding effect on vibronic spectra of isoquinoline in water solvent: Franck-Condon simulation and interpretation
(2016-10-28)
Liu, Yu-Hui
;
Wang, Shi-Ming
;
Wang, Chen-Wen
;
Zhu, Chaoyuan
;
Han, Ke-Li
The excited-state orientation hydrogen-bonding dynamics, and vibronic spectra of isoquinoline (IQ) and its cationic form IQc in water have been investigated at the time-dependent density functional theory quantum chemistry level plus Franck-Condon simulation and interpretation. The excited-state orientation hydrogen bond strengthening has been found in IQ: H2O complex due to the charge redistribution upon excitation; this is interpreted by simulated 1: 1 mixed absorption spectra of free IQ and IQ: H2O complex having best agreement with experimental results. Conversely, the orientation hydrogen bond in IQc: H2O complex would be strongly weakening in the S-1 state and this is interpreted by simulated absorption spectra of free IQc having best agreement with experimental results. By performing Franck-Condon simulation, it reveals that several important vibrational normal modes with frequencies about 1250 cm(-1) involving the wagging motion of the hydrogen atoms are very sensitive to the formation of the orientation hydrogen bond for the IQ/IQc:H2O complex and this is confirmed by damped Franck-Condon simulation with free IQ/IQc in water. However, the emission spectra of the IQ and IQc in water have been found differently. Upon the excitation, the simulated fluorescence of IQ in water is dominated by the IQ: H2O complex; thus hydrogen bond between IQ and H2O is much easier to form in the S-1 state. While the weakened hydrogen bond in IQc: H2O complex is probably cleaved upon the laser pulse because the simulated emission spectrum of the free IQc is in better agreement with the experimental results. Published by AIP Publishing.
Photoinduced Structural Dynamics in Laser-Heated Nanomaterials of Various Shapes and Sizes
(2008-11-06)
Yu, Pyng
;
Tang, Jan
;
Lin, Sheng-Hsien
;
應用化學系
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Department of Applied Chemistry
We examined photoinduced ultrafast structural dynamics such as coherent acoustic waves in many shapes of fcc metallic nanomaterials. Experimental data of nanosized thin films, prisms, spheres, rods, disks and pyramids from transient optical absorption/reflectance measurements were analyzed based on a combined Fermi-Pasta-Ulam model and two-temperature model. This work elucidates the structural dynamics induced by femtosecond laser heating, its size and shape effects on the period and phase of the excited acoustic phonon modes.