Browsing by Author "Yang, Ling"

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Absorption and fluorescence spectra of the neutral and anionic green fluorescent protein chromophore: Franck-Condon simulation
(2012-07-10)
Huang, Tsung-wei
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Yang, Ling
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Zhu, Chaoyuan
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Lin, Sheng Hsien
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應用化學系分子科學碩博班
Absorption and fluorescence spectra of the neutral and anionic green fluorescent protein (GFP) chromophore, namely p-hydroxybenzylideneimidazolidinone (p-HBDI), have been simulated using the Franck-Condon factors including inhomogeneous broadening of solvent effect. Ground and the first excited states were calculated by time dependent density functional theory with and without the polarizable continuum model environment. Simulated peak of the neutral/anionic p-HBDI at 380 nm (423 nm)/421 nm agrees with experiment value 370 nm (434 nm)/419 nm for absorption (fluorescence) spectrum. Simulated width of the neutral/anionic p-HBDI at 0.51 eV (0.54 eV)/0.57 eV agrees with experiment value 0.54 eV (0.66 eV)/0.56 eV for absorption (fluorescence) spectrum. (C) 2012 Elsevier B. V. All rights reserved.
Anharmonic Franck-Condon simulation of the absorption and fluorescence spectra for the low-lying S-1 and S-2 excited states of pyrimidine
(2012-05-25)
Yang, Ling
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Zhu, Chaoyuan
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Yu, Jianguo
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Lin, Sheng Hsien
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應用化學系分子科學碩博班
Intensities and profiles of vibronic spectra of the low-lying singlet excited states were investigated with anharmonic and harmonic Franck-Condon simulations for pyrimidine. The first-order anharmonic correction shows dynamic shift of spectra that is exactly same as difference of reorganization energy between ground and excited states. The first-order correction show intensity enhancement of absorption and intensity weakening of fluorescence for S-1 state, and dynamic shift is also significant. On the other hand, the first-order correction is negligible for S-2 state. The main spectral progressions are well described by totally symmetry modes v(6a), v(1) and v(12). One mode from non-total symmetry v(16a) contributes to the weak band at 16a(2) transition for S-1 state. Four ab initio methods were employed in simulation; CASSCF, CASPT2, DFT and TD-DFT, and coupled-cluster singles-doubles (CCSD) and the equation-of-motion (EOM-CCSD) methods. They all work well, but CASSCF method show the best agreement with experiment for the weak-band intensities. (C) 2012 Elsevier B.V. All rights reserved.
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
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Yang, Ling
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Zhu, Chaoyuan
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Yu, Jian-Guo
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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 of the A (1)B(2) -> X (1)A(1) dispersed fluorescence spectrum of fluorobenzene and its rate of the internal conversion
(2011-03-07)
He, Rongxing
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Yang, Ling
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Zhu, Chaoyuan
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Yamaki, Masahiro
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Lee, Yuan-Pern
By using three different hybrid exchange-correlation functionals containing 20%, 35%, and 50% of exact Hartree-Fock (HF) exchange of the density functional theory and its time-dependent extension plus the Hartree-Fock and the configuration interaction of single excitation methods, equilibrium geometries, and their 30 vibrational-normal-mode frequencies of the ground S(0)((1)A(1)) and the first excited S(1)((1)B(2)) states of fluorobenzene (FB) were calculated. The dispersed fluorescence spectrum and internal conversion (IC) rate of the A (1)B(2) -> X (1)A(1) transition were simulated by Franck-Condon (FC) calculations within the displaced harmonic oscillator approximation plus anharmonic and distorted corrections. The simulated spectral profile is primarily described by the Franck-Condon progression from the ring-breathing modes v(9) and v(10) which belong to totally symmetry modes. Anharmonic corrections simultaneously improve the intensity order of 9(1)(0) and 10(1)(0) bands and diminish 1(1)(0) transition that is fairly strong in harmonic simulations. It is concluded that the amount of Hartree-Fock exchange does impact the geometries and vibrational frequencies of FB molecule, but not the relative intensities of the transitions. It is anharmonic corrections that make the relative intensities of the transitions in good agreement with experimental results. Distorted corrections could assign most of the dominant overtones of out-of-plane nontotally symmetry modes, and the results agree well with the experimental assignments. Furthermore, it was found that the internal conversion rate is dominated by three promoting modes that are computed with lowing symmetry to C(1). By choosing dephasing width as 10 cm(-1) that is consistent with spectral simulation, we obtained the lifetimes of the A (1)B(2) -> X (1)A(1) de-excitation as 11 and 19 ns, respectively, from TD(B3LYP) and HF/CIS calculations in comparison with the experimental value 14.75 ns. (c) 2011 American Institute of Physics. [doi:10.1063/1.3559454]
Franck-Condon simulation of the A B-1(2) -> X (1)A(1) dispersed fluorescence spectrum of fluorobenzene and its rate of the internal conversion
(2011-03-07)
He, Rongxing
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Yang, Ling
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Zhu, Chaoyuan
;
Yamaki, Masahiro
;
Lee, Yuan-Pern
By using three different hybrid exchange-correlation functionals containing 20%, 35%, and 50% of exact Hartree-Fock (HF) exchange of the density functional theory and its time-dependent extension plus the Hartree-Fock and the configuration interaction of single excitation methods, equilibrium geometries, and their 30 vibrational-normal-mode frequencies of the ground S-0((1)A(1)) and the first excited S-1(B-1(2)) states of fluorobenzene (FB) were calculated. The dispersed fluorescence spectrum and internal conversion (IC) rate of the A B-1(2) -> X (1)A(1) transition were simulated by Franck-Condon (FC) calculations within the displaced harmonic oscillator approximation plus anharmonic and distorted corrections. The simulated spectral profile is primarily described by the Franck-Condon progression from the ring-breathing modes v(9) and v(10) which belong to totally symmetry modes. Anharmonic corrections simultaneously improve the intensity order of 9(1)(0) and 10(1)(0) bands and diminish 1(1)(0) transition that is fairly strong in harmonic simulations. It is concluded that the amount of Hartree-Fock exchange does impact the geometries and vibrational frequencies of FB molecule, but not the relative intensities of the transitions. It is anharmonic corrections that make the relative intensities of the transitions in good agreement with experimental results. Distorted corrections could assign most of the dominant overtones of out-of-plane nontotally symmetry modes, and the results agree well with the experimental assignments. Furthermore, it was found that the internal conversion rate is dominated by three promoting modes that are computed with lowing symmetry to C-1. By choosing dephasing width as 10 cm(-1) that is consistent with spectral simulation, we obtained the lifetimes of the A B-1(2) -> X (1)A(1) de-excitation as 11 and 19 ns, respectively, from TD(B3LYP) and HF/CIS calculations in comparison with the experimental value 14.75 ns. (c) 2011 American Institute of Physics. [doi:10.1063/1.3559454]
Quantum Chemical Calculations of Intramolecular Vibrational Redistribution and Energy Transfer of Dipeptides (GlyTyr and LeuTyr) and Applications to the RRKM Theory
(2013-07-01)
Yang, Ling
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Niu, Yingli
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Zhu, Chaoyuan
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Fujimura, Yuichi
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Shiu, Yingjen
Recently the quantum chemistry program can provide the anharmonic potentials for polyatomic molecules and clusters. It makes the quantum calculation of intramlecular vibrational redistribution (IVR) rates and intramolecular vibrational energy transfer possible. In the present paper, we apply the adiabatic approximation method to treat these two intramolecular energy redistribution processes. Using this method, we calculate the IVR rates of the dipeptides (glycyl tyrosine (GlyTyr) and leucyl tyrosine (LeuTyr)) and their cation radicals from the high frequency modes to the low frequency modes. Our theoretical results of the IVR lifetimes of the high frequency modes, like C-H, N-H, and O-H stretching modes, for both GlyTyr and LeuTyr molecules and their cation radicals are about 1 ps, 10 ps, and 100 ps, respectively. It provides theoretical support for the claim that IVR takes place prior to dissociation and the IVR rates are determined by the functional group rather than the degrees of freedom of the system. Thus the Rice-Ramsperger-Kassel-Marcus (RRKM) theory is suitable for investigating the photodissociation process of dipeptides. In addition, the calculated intramolecular energy transfer rate from O-H stretching mode of the C-termius of dipeptides to N-H mode of N-terminus is close to IVR rate.
Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP
(2018-07-01)
Zhang, Hao
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Yang, Ling
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Ma, Ying-Ying
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Zhu, Chaoyuan
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Lin, Shenghsien
The calcium-dependent beta-propeller proteins mammalian serum paraoxonase 1 (PON1) and phosphotriesterase diisopropyl fluorophosphatase (DFPase) catalyze the hydrolysis of organophosphorus compounds and enhance hydrolysis of various nerve agents. In the present work, the phosphotriesterase activity development between PON1 and DFPase was investigated by using the hybrid density functional theory method B3LYP. Based on the active-site difference between PON1 and DFPase, both the wild type and the mutant (a water molecule replacing Asn270 in PON1) models were designed. The results indicated that the substitution of a water molecule for Asn270 in PON1 had little effect on the enzyme activity in kinetics, while being more efficient in thermodynamics, which is essential for DFP hydrolysis. Structure comparisons of evolutionarily related enzymes show that the mutation of Asn270 leads to the catalytic Ca2+ ion indirectly connecting the buried structural Ca2+ ion via hydrogen bonds in DFPase. It can reduce the plasticity of enzymatic structure, and possibly change the substrate preference from paraoxon to DFP, which implies an evolutionary transition from mono- to dinuclear catalytic centers. Our studies shed light on the investigation of enzyme catalysis mechanism from an evolutionary perspective.