Browsing by Author "Huang, Gou-Tao"

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Analyses on Molecular Properties of the Diamidinate Cr-I-Cr-I Complex by Multireference and DFT Approaches
(2019-09-12)
Huang, Gou-Tao
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Yu, Jen-Shiang K.
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交大名義發表
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生物科技學系
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生物資訊及系統生物研究所
The model system of the diamidinate Cr-I-Cr-I complex is investigated by wave function theory (WET) and Kohn-Sham density functional theory (KS-DFT). The multireference perturbation theory (RASPT2) estimates a stabilization energy of ca. 20 kcal mol(-1) for the delta bonding. The multiconfiguration pair-density functional theory (MC-PDFT) with the ftPBE functional well predicts the singlet energy curve comparable to the RASPT2 level. For the KS-DFT scheme based on a single determinant, seven functionals including BP86, BLYP, PBE, B3LYP, M06-L, M06, and omega B97X-D are assessed: two types of functionals are classified according to the nature of the restricted and broken symmetry potential energy curves. The broken symmetry scheme with the type I functionals can give good results for the energy curve in agreement with the multireference calculations. In regard to the metal-metal bonding, the restricted KS-DFT calculations performed by all of the seven functionals yield inferior description due to the lack of significant multiconfigurational character. The Mayer bond order, the electron localization function, and electron density predicted by the broken symmetry formalism with the type II functionals are consistent with those obtained with the multireference theory.
Can the Radical Channel Contribute to the Catalytic Cycle of N-Heterocyclic Carbene in Benzoin Condensation?
(2018-12-21)
Hsieh, Ming-Hsiu
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Huang, Gou-Tao
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Yu, Jen-Shiang K.
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交大名義發表
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生物科技學系
NHC can catalyze benzoin condensation via the key Breslow intermediate. EPR spectroscopy recently confirmed the existence of the radical species, but its catalytic role is still unclear. Herein, we use density functional approaches to study the radical-associated pathway in comparison with the nonradical mechanism reported previously. Theoretical investigations show that the nonradical path (Delta G(double dagger) = 18.7 kcal/mol) is more kinetically favorable than the radical route (Delta G(double dagger) = 27.6 kcal/mol), which is initialized by the hydrogen abstraction from the Breslow intermediate by benzaldehyde, leading to a radical pair. The product formation is thus dominated by the nonradical pathway. In addition, the Breslow intermediate is less stable than its keto form, which blocks the benzoin condensation, and the radical species could play an important role in assisting the tautomerization and promoting the catalytic reaction.
Catalytic Roles of Histidine and Arginine in Pyruvate Class II Aldolase: A Perspective from QM/MM Metadynamics
(2017-12-01)
Huang, Gou-Tao
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Yu, Jen-Shiang K.
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生物科技學系
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生物資訊及系統生物研究所
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分子醫學與生物工程研究所
The retro-aldol reaction catalyzed by pyruvate class II aldolase is investigated with QM/MM metadynamics; this enzyme transforms the substrate of 4-hydrox-y-2-ketoacid into pyruvate and aldehyde through the aldol cleavage. The hydroxyl group of the substrate is deprotonated by His45 with the aid of the metal-bound water, while the metal-bound hydroxide proposed in the literature is observed as a transient species. The deprotonation appears to enhance substrate binding between the deprotonated substrate and the active site. The reactive alkoxide is further stabilized by the salt bridge of Arg70-Asp42, facilitating the following aldol cleavage. The simulations show that the C-C bond cleavage is the rate-determining step, and the calculated barrier of approximately 14 kcal mol(-1) agrees reasonably with experimental data.
Enzyme Catalysis that Paves the Way for S-Sulfhydration via Sulfur Atom Transfer
(2016-05-26)
Huang, Gou-Tao
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Yu, Jen-Shiang K.
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生物科技學系
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生物資訊及系統生物研究所
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Department of Biological Science and Technology
S-sulfhydration is generally anticipated to proceed through the transfer of the SH group (Nu-SH center dot center dot center dot S--R -> Nu(-)center dot center dot center dot HS-S-R). The other route involves the sulfur atom (5) transfer between two sulfhydryl anions (Nu-S-center dot center dot center dot S--R -> Nu(-)center dot center dot center dot S--S-R) and is considered electrostatically unfavorable. Mercaptopyruvate sulfurtransferase (MST, PDB code: 4JGT) catalyzes sulfur transfer from mercaptopyruvate to sulfur acceptors, and the first step of the reaction is the formation of cysteine (Cys248) persulfide via S-sulfhydration. Mechanistic studies on S-sulfhydration in MST using QM/MM methods show that the sulfur atom transfer initialized by the deprotonation of the Ser250/His74/Asp63 triad is kinetically preferred to the SH-promoted sulfur transfer. The calculated barrier of approximately 16 kcal mol(-1) for the S-0 transfer agrees well with experimental results. The electrostatic repulsion during the S-0 transfer can be sophisticatedly reduced by the aid of the Cys248-Gly249-Ser250-Gly251-Val252-Thr253 (CGSGVT) loop. Electrostatic potentials and frontier orbitals are also analyzed for the persulfide anion surrounded by the loop. The sulfur atom transfer which is seldom regarded possible is therefore facilitated with the assistance of the triad and the loop in the enzyme.
Reversible Cleavage/Formation of the Chromium-Chromium Quintuple Bond in the Highly Regioselective Alkyne Cyclotrimerization
(2017-11-27)
Huang, Yu-Siang
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Huang, Gou-Tao
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Liu, Yao-Lun
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Yu, Jen-Shiang K.
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Tsai, Yi-Chou
Herein we report the employment of the quintuply bonded dichromium amidinates [Cr{(2)-HC(N-2,6-(Pr2C6H3)-Pr-i)(N-2,6-R2C6H3)}](2) (R=iPr (1), Me (7)) as catalysts to mediate the [2+2+2] cyclotrimerization of terminal alkynes giving 1,3,5-trisubstituted benzenes. During the catalysis, the ultrashort Cr-Cr quintuple bond underwent reversible cleavage/formation, corroborated by the characterization of two inverted arene sandwich dichromium complexes (-(6):(6)-1,3,5-(Me3Si)(3)C6H3)[Cr{(2)-HC(N-2,6-(Pr2C6H3)-Pr-i)(N-2,6-R2C6H3)}](2) (R=Pr-i (5), Me (8)). In the presence of sigma donors, such as THF and 2,4,6-Me3C6H2CN, the bridging arene 1,3,5-(Me3Si)(3)C6H3 in 5 and 8 was extruded and 1 and 7 were regenerated. Theoretical calculations were employed to disclose the reaction pathways of these highly regioselective [2+2+2] cylcotrimerization reactions of terminal alkynes.